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Continuity
(at around 32 mins) In the scene from behind Dr. Grant we can see the cow being lifted straight up. You can see that the cow is rather close to Dr. Grant. Then the scene cuts and the cow is already in the middle of the top of the Velociraptor paddock. Judging from the distance between Dr. Grant and the paddock from the previous wide-shot, and the fact that Dr. Grant made no big moves, the crane couldn't pass that distance between the two shots.
(at around 1h 3 mins) When they arrive at the T. rex cage right before the black out, we can clearly see the ground inside the cage is approximately flush with that outside the cage. But when the T. rex escapes and begins to terrorize the two trucks, the ground in the cage is shown to be at least 100 feet below where it was before.
Hammond has a pronounced Scottish accent at the start of the film, which deteriorates markedly in just a couple of scenes. By the end of the film he has an upper class English accent.
(at around 1h 3 mins) Gennaro runs off and leaves Lex and Tim in the Explorer when the T. rex appears, and leaves the car door open. Later, we see the same vehicle through the windscreen of Grant and Malcolm's vehicle and the same door is closed. Later on still, Tim shuts the door which is what attracts the T. rex' attention.
(at around 1h 25 mins) When Ellie enters the cafeteria where Hammond is eating ice cream the ceiling fans are working despite the power being out.
(at around 1h 4 mins) The goat's leg mysteriously disappears just before the T. rex smashes into the roof of the car.
(at around 25 mins) The mosquito that is encased in amber, and from which the DNA sample is extracted is male. This is evident from the "bushy" look of the antennae. Female mosquitoes have far fewer hairs on their antennae, and so the distinction is easily made. Only females drink blood, as it is needed to produce eggs. There would not have been any dinosaur DNA in the male to extract. To make it worse, in that species of mosquito, Toxirhynchites, both the males and females are flower feeders, and would therefore have no blood, or dinosaur DNA in their stomachs.
The spaces between the wires on the electric fence are far enough apart for Tim to crawl through the fence, and not have to climb over.
Dominican amber is famous for its quality, but it was only formed 20 million years ago, long after the dinosaurs had died out, so you could never find a prehistoric mosquito that had fed on dinosaur blood there, and even then, one that was completely uncontaminated, which would have been amplified along with the DNA, as well as too degraded. There is nothing to compare it with.
At the beginning of the film we are shown an amber mine in the Dominican Republic. This amber is only 45 million years old, Hammond would never bother buying the amber from there as dinosaurs disappeared from the fossil record 65 million years ago.
(at around 1h 17 mins) The way the car "slides" down the tree as Grant and Tim are climbing down is very unrealistic. Rather than hugging the trunk like it does, the branches (some of which are thick enough) would deflect it away from the trunk.
Many of the animals are depicted inaccurately, but this can be explained within the storyline - the InGen scientists have made mistakes or deliberate alterations to the species they cloned. They combined Velociraptor with Deinonychus, made Dilophosaurus a dwarf, and gave Brachiosaurus a chewing ability.
(at around 5 mins) Dr. Grant is shown at the beginning of the film excavating a velociraptor in Montana. True velociraptors have only been found in central Asia, but Montana was home to the closely related Deinonychus, which some paleontologists considered to be the same as Velociraptor at the time the original Jurassic Park novel was written. For the movie, they kept the incorrect name.
Contrary to Hammond's boast that he "Spared no expense", he is shown on numerous occasions to have cut corners on areas of the park. For example, Nedry complains (or boasts) that nobody else could "network 8-connection machines and debug 2,000,000 lines of code" for what he "bid for this job", implying that Hammond sold the security programming job to whoever promised him the cheapest price. Both Muldoon and Arnold are also shown complaining to Hammond, even occasionally clashing, about the park's numerous security issues not being addressed. This isn't so much a goof, though, as just showing the flaw in Hammond's ignorance, or perhaps intended as an ironic comment on how he spent so much time and money on the park's dinosaurs that, contrary to his boasts, he ignored other important areas of the operation.
If Site B was where the dinosaurs were bred (In The Lost World: Jurassic Park (1997)) then why was the velociraptor born on Isla Nublar? Hammond wanted to create the illusion that all of the animals were, in fact, created on Isla Nublar. It isn't until The Lost World that it was revealed that Site B on Isla Sorna was where the large industrial compound producing thousands of embryos for a single viable one was located. This is explained in the novel but not mentioned in any of the movies.
(at around 58 mins) When initially passing the Tyrannosaur paddock, the cars are heading right. When the cars return due to the hurricane coming, the cars are heading left. There could be an emergency turnaround point in the track that wasn't shown. Additionally, the tour had only been through 3 its scheduled stops, so one could assume they weren't very far into the park when they needed to return. Reversing the vehicles and going back the way they came was likely safer than sending them through the remaining paddocks of the park, if for no other reason than it would've take much less time.
(at around 54 mins) "Surveillance camera" views displayed on computer monitors are obviously video clips that are being played back from disk (progress meter on the bottom).
(at around 1h 40 mins) In the climbing of the electric fence scene, there is a shot where it is plainly seen that this is a mere section of fence, and the actors could easily walk around it.
(at around 34 mins) There is an absence of blood on the shredded harness used to hold the cow after it has been fed to the raptors, despite the violence of the feeding scene.
(at around 1h 2 mins) When the goat leg falls on top of Tim and Lex's car, the severed end of the leg is cleanly cut, as if with a knife. Given that every time other we see the T. Rex feed it shakes its prey violently, like a shark would, the goat leg should be ragged and rent. The fact that it shook it's prey every other time, doesn't necessarily mean it would that time. The goat could have been small enough that the T-Rex didn't think it was necessary to shake it to death.
(at around 1h 24 mins) When Grant and the children are sitting in the tree overlooking the Brachiosaurs, and again when climbing the electric fence (at around 1h 40 mins), the soles of Grant's boots can be seen and are completely clean and free of any mud or debris.
(at around 1h 50 mins) After the kids escape the kitchen they're in the control room with Alan and Ellie. Lex is getting things running on the computer while Alan and Ellie are trying to hold the door closed to keep the velociraptor out. Ellie tries to get the gun with her foot but cannot get hold of it. Since Tim wasn't doing anything there was no reason he couldn't have gotten the gun for her.
About 1:55: When Grant calls Hammond and gunshots ring out. Quick shot of three bullet holes in the glass. Grant drops the gun to run and the camera shows a brief shot of the gun on the floor, with shotgun shells coming out of it. Shotgun pellets would not make neat round bullet holes in the glass.
(at around 5 mins) At the dig site where the lawyer shows up (only to find that Grant is not there), they call the manager to a find. The manager tells people to aim their light on the find. Looking at the directions the people are aiming their lights, only one light hits the mosquito in amber.
Dr. Grant states to his colleagues/crew that Velociraptors have more in common with modern day birds than reptiles. He then goes on to provide anatomical examples to support his argument, but then states "even the word 'raptor' means 'bird of prey'". This is not a credible argument because it has nothing to do with the anatomy or physiology of birds compared to Velociraptors.
(at around 1h 6 mins) When the T. rex is attacking the car with Lex and Tim, in a shot through the roof wind-shield, you can hear them scream. However, their mouths stay closed.
(at around 1h 55 mins) When Lex falls through the ceiling, she is screaming but her mouth isn't moving.
(at around 45 mins) When the goat is offered to the T. rex, you hear the bleating sound of a sheep as opposed to a goat's bleating sound.
During examining the sick triceratops, Harding gives Ellie a flashlight to check the animal's eyes. Offscreen, a click is clearly heard to signal the flashlight being turned on, but the flashlight used is a Maglite brand which twists to turn on rather than clicking.
(at around 32 mins) When the raptors are being fed for the viewing of the visitors, a crew member's white shirt can clearly be seen shaking the leaves in the pit as the raptors attack their prey.
(at around 1h 45 mins) Arm of crew member when the velociraptor first enters the kitchen. The velociraptor was actually a full, but generally immobile, robot.
(at around 1h 6 mins) A studio light and a potted tree are briefly visible in the background when the T. rex flips over Lex and Timmy's car, as well as a number of cables and wires attached to the car. These have been digitally erased in the movie's 3D re-release in cinemas and on Blu-Ray.
(at around 1h 45 mins) The raptor looks through the kitchen window with a spray of breath on the glass. Just before that, you can hear and see the digital clapper and the man holding it reflected on the door.
(at around 1h 18 mins) Stage light reflected on the hood of the Explorer when it hits the bottom of the tree.
(at around 13 mins) Nedry is shown seated at a beachfront cafe behind the caption "San Jose, Costa Rica". San Jose is a landlocked cosmopolitan capital of almost 1 million people, situated 50 miles from either coast, without any adjoining lakes.
(at around 40 mins) The tropical storm is reportedly some distance west of the island. At the latitude of Costa Rica, tropical storms move east to west. The storm should have moved away from the island.
(at around 1h 20 mins) Just after Malcolm is rescued, you see him sitting in the back of the jeep in the T. rex area next to the other vehicle viewing the tremors in the water. In the next shot he is hurrying the others to come to the vehicle and they are in a completely different area of the park.
When Ellie and Muldoon arrive at the Tyrannosaur enclosure, they pull up from behind the second car. During the tour, the vehicles came up from the far side of this enclosure, and are now turned around to head back towards the visitor's center. Ellie and Muldoon came from that direction, so they should actually be pulling up ahead of where the car with the children was.
In the final scene, the helicopter supposedly is flying towards the mainland. Since it flies directly towards the sun instead (and it has to be a sunset) and Isla Nublar is located in the Pacific, the helicopter actually moves away from the South American continent.
When the T. rex first gets out, it claws open the fence and walks through the opening; however, when Dr. Grant and Lex go through the same spot in the fence, there is a significant drop (large enough for a jeep to drop past them and into a tree that Dr. Grant then climbs to rescue Tim). The dropoff that Dr. Grant and the kids scale down would have made the fence too tall for the T. rex to reach or even see.
(at around 20 mins) The plot centers around finding dinosaur blood in fossilized mosquitoes trapped in amber. However, our first encounter with extinct life comes when Ellie examines a leaf and says "This 'veriforman' species has been extinct since the Cretaceous." No mechanism is provided for how they could have cloned the plants, given that mosquitoes don't drink plant juices. It is possible that DNA could have been extracted from the amber (hardened tree-sap), but this still doesn't account for other types of plants, such as ferns and bushes.
(at around 1h 45 mins) When Tim and Lex arrive at the visitor center, after their "tour", they find a entire buffet set with desserts. But all personnel left the night before and only the people in the control-room have been around. Hammond and Ellie ate dessert the night before, but it should have gone bad or melted until the children arrived. No staff of the kitchen seem present or around either. To leave all this food out seem without logic. Especially since no one has eaten from it or intend to do so.
It is quite unlikely that a really important room like the control room doesn't have a manual (or at least an independently powered) lock which would be operational in the event of a power outage.
(at around 30 mins) Dr Wu claims "all vertebrate embryos are inherently female". This is inaccurate. In fact, it would have made more sense to breed the dinosaurs all-male, because there are far fewer variables, and may have eliminated the danger of breeding altogether.
(at around 57 mins) In the embryo freezing chamber, Tyrannosaurus rex is spelled with only one "N" instead of two. Also, Stegosaurus is spelled "Stegasaurus".
(at around 42 mins) In the scripted audio tour, the narrator refers to the dilophosaurus as poisonous, when in fact if the method of toxin exchange is spitting or biting, then it is actually venomous.
(at around 46 mins) Grant says; "T-Rex doesn't want to be fed. He wants to hunt. Can't just suppress 65 million years of gut instinct". However he has it the wrong way round; dinosaurs had 200 millions years of gut instinct; 65 million is the period for which they were extinct.
(at around 5 mins) During his dig in Montana, Grant makes three mistakes: First, he unearths a velociraptor in Montana. Velociraptor remains have only been found in Asia. Second, he declares that velociraptor was a pack hunter. All velociraptor remains have been found alone, indicating exactly the opposite. Both of these, however, are accurate claims about Deinonychus, on which Michael Crichton modeled his velociraptors. Thirdly, Grant says that raptor means "bird of prey." It is actually Latin for thief. (The English word rape has the same root, and originally meant theft.) The first velociraptors were found around egg nests, and paleontologists thought it was an oviraptor (egg thief). They subsequently concluded that the eggs were in fact velociraptor eggs, indicating that the animals cared for their young, rather than abandoning them, as many had previously thought.
(at around 8 mins) As Dr. Grant lectures the cynical boy at the dig site about the velociraptor, he says that the velociraptor's claw was used to eviscerate and tear its victims apart, as opposed to going for the neck like many of today's predators. The fossilized remains of a velociraptor caught in a feud with its prey clearly show the velociraptor stabbing the prey in the neck with its claw. The Truth About Killer Dinosaurs (2005) also conducted an experiment to see if the claw could eviscerate flesh. It couldn't.