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Incorrectly regarded as goofs
(at around 42 mins, extended version only) As the dropship heads to the planet, Cpl. Hicks appears to be asleep. When the ship enters the atmosphere and the marines get ready to deploy, he is clearly awake. In the next shot he is still asleep. Finally Apone says "Somebody wake up Hicks." This is all meant to demonstrate how seasoned a soldier Hicks is: that he can "sleep" through the drop. At no point is he ever actually asleep, he's just very relaxed. He opens and closes his eyes as the conversation interests or disinterests him. Apone is simply making a joke about this.
(at around 1h 30 mins) When Ripley tries to break the glass in the med lab there is a scuff mark on the glass before her first swing. After this finishes, the mark disappears and we see Ripley actually making the mark with her second swing. (This goof was digitally corrected for the blu-ray edition)
(at around 1h 45 mins) In the elevator escape scene where Hicks gets acid sprayed, he holds his gun in front of his face and turns his head to the left. Any acid burns he got would have been to the right side of his face. As they fight to remove his melting chest armor, there are no acid marks on his face. When they leave the elevator, the acid burns are on the left side of his head, instead of the right side.
(at around 2h 10 mins) After the Queen falls down the airlock, the sharp end of her tail is missing (obviously unintentional, and overlooked or not repaired by the crew). The tip is back on moments later as she's tumbling through space.
(at around 2 mins) In Alien (1979), the computer displays have an old-fashioned "teletype" clicking noise when they show data on their screens. However, when the screen in the Nostromo shuttle comes to life at the beginning of Aliens, the display looks and sounds more modern like the other computer screens seen later in the film - even though 57 years have passed and the equipment in the shuttle has not been touched all that time.
(at around 1h 7 mins) After an alien smashes a hole through the triangular windshield on the APC during the escape from under the cooling tower the windshield is then shown with an unbroken windshield as it exits on to the planet surface.
(at around 31 mins) When the dropship is released, it is shown to be falling immediately as if in full gravity. However, since the Sulaco is placed on a stationary orbit, the dropship should remain in place upon releasing the clamps. An additional burn would seem to be necessary to initiate breaking orbit. However, a burn is not the only way the dropship could be moved out of the clamps. Other technology could well do it, and might be preferable to a burn that close to the ship. For example using electromagnets to push it. Or artificial gravity may be able to be reversed, or a similar technology could be used create a repulsive force. However, if any of these methods were employed, the separation of the drop ship would have been far smoother than it was and it was obviously an attempt to show it responding to the planet's gravity.
(at around 56 mins) The reason given for removing the marine's ammunition is that the facility is a giant fusion reactor and damaging the cooling system will cause a thermonuclear explosion. A fusion reaction does not use or produce fissionable material so it cannot cause a thermonuclear explosion.
(at around 31 mins) The landing sequence is incorrect. The dropship is seen accelerating while deorbiting, such acceleration would send it to a higher orbit. Deorbiting needs deceleration from the orbital speed. The dropship should have fired retro-rockets or it should have turned backwards to use the main thrusters for deceleration. Moreover, if the Sulaco is exactly above the colony (as stated in the novelization), the dropship should have done a vertical drop (relative to the planet) or should have completed a full orbit while descending to end up right above the colony.
(at around 2h) At the end of the movie, the compound explodes and the survivors escape in a shuttle. We see that brightness of the explosion shines on their face. But in fact, the explosion and the light source is behind, so there's no way their sight would be affected by the brightness.
(at around 2h 10 mins) In the airlock shaft scene at the end, it is preposterous to think that Ripley could hang on to the ladder as the ship is violently decompressing, whereas the queen Alien (which is hundreds of times stronger than Ripley is) could not. Not only could Ripley hold on, but she manages to climb back up out of the shaft while the decompression is taking place, making it even more absurd.
(at around 1h 40 mins) When the aliens capture Newt and Ripley tries to go after her, Hicks holds her back and tells Ripley that they can track Newt using the tracking device. Hicks gave the tracker band to Ripley and didn't witness Ripley giving it to Newt so he wouldn't have known this. However, he didn't witness it onscreen; Ripley obviously told him about it offscreen.
(at around 1h 29 mins) When Ripley goes back to medical to join Newt, she lays her rifle on top of the bed and then lays down on the floor beside Newt. Moments later she looks to break the glass but finds her rifle laying on a table on the other side of the glass. The scene makes it clear that Burke entered while she and Newt were asleep and laid down the opened containment cylinders with the facehuggers inside of them; it's fairly obvious that he moved her rifle out of the room as well (note Ripley's expression when she sees her rifle).
In Alien (1979), LV-426 is adjacent to a huge planet with Saturn-like rings (which it probably orbits). Such is its size, it can even be viewed from the surface (i.e. when the Nostromo crew investigate the alien ship). The ringed planet is never seen in this film, either from space or from the surface of LV-426 because James Cameron simply chose not to depict it from any angle.
(at around 42 mins, extended version only) As the dropship heads to the planet, Cpl. Hicks appears to be asleep. When the ship enters the atmosphere and the marines get ready to deploy, he is clearly awake. In the next shot he is still asleep. Finally Apone says "Somebody wake up Hicks." This is all meant to demonstrate how seasoned a soldier Hicks is: that he can "sleep" through the drop. At no point is he ever actually asleep, he's just very relaxed. He opens and closes his eyes as the conversation interests or disinterests him. Apone is simply making a joke about this.
(at around 16 mins, extended version only) It may seem like a whole lot of coincidence that the colonists on LV-426 happen to find the derelict ship just after Ripley has been found. But as made clear, Newt's family finds the derelict ship not by chance, but as a result of orders given by the colony technician seen in Operations, who directed the "Mom and Pop survey team" there. He himself was given orders by "some honcho in a cushy office on Earth" who told him to "go look at a grid reference." That honcho, of course, was Burke, whose directive Ripley discovered in the colony log.
(at around 2h 10 mins) When Bishop saves Newt from being sucked out of the airlock, part of Lance Henriksen's real torso can be seen beneath the false one, emerging from a hole in the floor. (James Cameron acknowledges this error on the DVD commentary; the goof was digitally corrected for the 2010 Blu-ray release.)
(at around 21 mins) When Bishop is "doing the thing with knife" the scene is sped up to give the impression that Bishop is lightning fast. Apone can be seen rocking his head back and forth, also at a ridiculous speed.
(at around 1h 55 mins) When Ripley turns to find herself in the Queen's chamber, Newt's hand is rigid because she is holding a lightweight Newt dummy.
(at around 56 mins) Gorman states that the M41A Pulse Rifle fires 10mm explosive tipped case-less ammunition, several times throughout the film, you can clearly see casings leaving the ejection port of the pulse rifles. Caseless ammunition, as the name suggests, doesn't have a shell casing to eject; it's an integral part of the ammunition and either exits the barrel along with the round itself or is consumed by the act of firing. This is because the marine's prop weapons were made by combining modified Thompson SMGs and Benelli shotguns, both of which use conventional "cased" ammunition.
(at around 4 mins) When the salvage crew shines a light onto Ripley's face while she is sleeping at the beginning of the movie, her right eyelid twitches. Although people's eyelids twitch all the time when they are asleep, Ripley is frozen in cryogenic suspension - not merely asleep.
While it may seem that there is no reason for Bishop to sleep in cryostasis like the rest of the crew since he is not on the mission covertly (like Ash was in Alien (1979)), it is plausible that he is programmed to pass for human by default. In an interview, Lance Henriksen explained the original idea was to have Bishop remain awake during the trip, and passing the time by doing a "thousand thousand push-ups", but this was replaced with the "thing with the knife" to demonstrate his prowess as an android. However, there is still no logical explanation for having him sleeping with the rest of the crew when it would be far more prudent to have him awake and monitoring the ship's systems in case of emergencies (much like David and Walter do in the prequels "Prometheus" and "Alien: Covenant").
(at around 1h 25 mins) After Vasquez cuts a hole in the conduit to allow Bishop to crawl to the transmitter, the metal cut out segment falls into the conduit pipe through the hole. When Vasquez replaces the cut out piece, it does not fall through. This is because she rotated the asymmetrical piece so that it would fit. But if she did not replace it in exactly the same way it was cut, it wouldn't have fit so neatly into the cut-out hole.
(at around 1h 45 mins) In the elevator when Hicks shoots the alien at point blank range, he gets covered in its acid blood. Ripley is standing right next to him and yet doesn't get even a drop on her.
(at 10:54 in the director's cut) When Ripley is being questioned by the company officials, the records of the dead Nostromo crew from the first movie are displayed on the screen behind her. Even though these are supposed to be official records, there are frequent typos: In Parker's record, the word "and" is misspelled as "aand" twice, and "throughout" is misspelled as "throuhout."
Ripley presses two buttons on the loader to open the inner doors of the airlock of the Sulaco.
While convenient for the plot, the possibility of accidentally pressing them (and those on other loaders) at any time make this quite a safety-related design flaw.
Even worse, and although not shown, presumably when Ripley has thrown the alien 'queen' into the airlock she intended to open the outer doors in the same way as she definitely wouldn't have climbed out of the loader to do so.
While convenient for the plot, the possibility of accidentally pressing them (and those on other loaders) at any time make this quite a safety-related design flaw.
Even worse, and although not shown, presumably when Ripley has thrown the alien 'queen' into the airlock she intended to open the outer doors in the same way as she definitely wouldn't have climbed out of the loader to do so.
(at around 20 mins, extended version only) When Newt's mother is calling in the mayday, she is heard saying "Alpha zero two four niner" repeatedly, but the second time she says it her mouth is saying something else.
(at around 1h 40 mins) During the ventilation shaft scene towards the end of the movie Vasquez tells Gorman "you always were an asshole". However, you do not see her lips moving at the end after the camera angle changes.
(at around 1h 6 mins) After the first contact with the Aliens at the processing station and Drake is killed, Vasquez is being held back by Hicks near the door of the APC. He yells that Drake is gone and she says, "No he's not," but her mouth does not move in sync with the line.
(at around 1h 1 min) While Frost is falling after being set on fire and falling over railing, just before the shot cuts away, in the bottom left corner you can see a crewmen moving and a boot sticking out from the shadows.
(at around 1h 55 mins) When Newt is cocooned and Ripley finds her, two suspension lines are visible on the first alien that comes bounding off the walls to attack them.
(at around 31 mins) When the team is descending down to the planet, camera lights and screens are clearly visible in the reflection off Ferro's mirrored sunglasses, and in several shots.
(at around 26 mins) After Spunkmeyer loads the missile, he calls "Clear behind!" and walks the power loader backward. A thick cable can be seen attached to the loader's left foot. (The loaders are supposed to be free-standing.)
There are several instances in the film of someone shooting an alien at point-blank range, yet not getting any of their acidic blood on them.
(at around 9 mins) The inquest had gone on for "three and a half hours", yet no one mentioned that LV-426 had been colonized for over twenty years. It could have been that the board needed to hold Ripley accountable for the willful destruction of the Nostromo for insurance reasons, they obviously felt it was in nobody's best interest to broach the subject. However, the colonization of LV-426 was not classified information and if anything would have strengthened the company's case against Ripley. It seems logical that somebody would have mentioned it sooner.
It doesn't make sense that all Sulaco personnel go down to the planet at once. And there are no additional crew or a reserve team of marines standing by to offer aid and assistance, in the likelyhood the first team become stranded and need immediate retrieval.
According to the Alien Universe Wikia, Xenopedia, the Queen Alien weighs about ten tons. How she can hide inside the landing gear of a drop ship and no one notice the extra weight or imbalance in the ship's aerodynamics would be impossible. (Note: the ten tons may include a functioning egg sac, which the Queen had left behind for the chase. However, the Queen would still be heavy enough to affect the weight of the ship)
Ripley knew there were thousand of eggs on the derelict space craft, as she states this during the inquest. So when she asks who's laying the eggs her first thought should have been the derelict eggs not some possible organism responsible for doing it.
(at around 1h 1 min) Before the marines' final stand in Operations, their motion trackers cannot tell if the aliens are on the same level. Therefore the aliens' ability to surprise and slaughter the marines hinges entirely on character error. Ripley references the earlier scene, in which they examined the floor plans, with the possibility that the aliens came in through something they missed or was not in the plans, that being the space above the suspended ceiling vents. By this time, the stress of the situation could have caused everyone to forget this, unlike the calmer floor plan scene.
(at around 13 mins, extended version only) During the inquest, Van Leuwen refers to Ripley's company ID number as NOC14472 while the data screen in the background displays NOC14672.
(at around 1h 45 mins) Just after Newt is taken, Ripley screams at Hicks that the aliens "don't kill you", implying that everyone they encounter is taken for implantation.
However, on a number of occasions in movies in the franchise, particularly in Alien (1979), the aliens used their secondary jaws to punch holes in their victim's head.
However, on a number of occasions in movies in the franchise, particularly in Alien (1979), the aliens used their secondary jaws to punch holes in their victim's head.
Ripley seems to have a remarkably forgiving attitude toward The Company, considering she saw a directive issued by them to Ash in Alien (1979) that stated 'crew expendable' with regard to herself and her shipmates.
(at around 1h 25 mins) It has been established that Bishop is an android (or artificial person). When he volunteers to go into the tunnel to the colony transmitter to bring down the spare dropship. When he commences his crawl, you hear him breathing heavily. He is programmed to pass for a human by default. However, Bishop was alone during his crawl through the pipe. He doesn't have to "act" like a human. Furthermore, any excess noise he makes is more likely to attract the attention of the aliens.