Superman and Lois change clothes at the Fortress of Solitude, despite the fact that they brought no luggage.
(at around 1h 55 mins) When Superman takes Lois flying for the last time, scenes from Superman (1978) are used. She is wearing the blue outfit she wore in that movie, not the clothes she wore during the ordeal with the three Krypton villains at the Fortress of Solitude.
The film begins with a reprise of the trial of Zod, Ursa, and Non from Superman (1978). Jor-El's dialogue is completely different. The error is rectified in the Richard Donner cut, which restored Marlon Brando's original footage and dialogue.
(at around 57 mins) When the county sheriff and his deputy first encounter Zod, Ursa, and Non, after discharging the shotgun, Zod throws it and it lands in front of the passenger side rear wheel. When Non lifts the patrol car to retrieve the weapon, it has moved behind the wheel.
(at around 18 mins) When Superman stops the Eiffel tower elevator from falling, Lois jumps straight down, as though onto some kind of platform. However Superman flew straight up through the tower. She should have had to jump over to the side at least a couple of feet in order to find anything solid to stand on.
(at around 39 mins) When the boy at Niagara Falls begins to fall it takes approx. 28 seconds for Superman to catch him. Since the fall would have been only about 200 feet it would have taken the boy around 4 seconds to hit the water.
Superman, Zod, Ursa, and Non's clothes flap about as they fly in space. There is no wind or air in space to make clothes flutter.
(at around 19 mins) Zod and company are released by the Phantom Zone being "shattered" by a shock wave from the nuclear device. These kind of shock waves only occur in an atmosphere and would not occur in space.
(at around 28 mins) When the astronaut tries to escape by jumping into the lunar module, Non grabs the leg of the descent stage to stop him. In reality, the descent stage is left behind and the ascent stage detaches in order to leave the Moon's orbit; holding the legs would do nothing.
(at around 26 mins) Ursa speaks to the astronaut aloud, despite there being no air on the Moon to form words or carry sound.
When Superman finds out about Zod, he goes back to the Fortress of Solitude to recover his powers. How he does it is never shown, though it is implied that the green crystal Lois accidentally dropped earlier somehow recovered and reactivated the Fortress and its systems. In the Richard Donner cut, Jor-El gives his remaining energy to Superman so he can recover his powers.
Clark yells out "Father!", in the fortress of solitude after realizing his disadvantages, due to stripping his powers. He however explained it to the hologram of his mother, Lara, not at all the hologram of his father, Jor-el. This is because the original scene (of his powers being stripped) was filmed with the Jor-el (Marlon Brando) character, it was re-shot with the Lara (Susannah York) character.
One of Superman's powers is super speed and he can get to places around the world quickly, yet it appears to take him a while to get from Metropolis (which appears to be on the East Coast of the U.S.) to Paris, France. The film doesn't confirm that the Paris scene is right after the Metropolis scene (where his newspaper workers inform him of the crisis), it's likely he was informed of it at some point during the Paris scene.
(at around 1h 18 mins) When Lois and Clark are driving from the Fortress of Solitude after Superman gives up his powers, the car is actually from Superman (1978). It's from the scene when Lex Luthor flips the car by remote control so he can stop one of the missile convoys, and steal the missile. Note the blacked-out windshield, to give the illusion of no one at the wheel.
(at around 8 mins) When Zod flings the cosmonaut up and then yanks his airline down, the line falls at normal "earth gravity" speed.
(at around 1h 1 min) In East Houston, when Zod lifts the man into the air, the crash mat below him is clearly visible when he drops back down.
(at around 30 mins) As Non throws down the flags at the end of the scene on the Moon, the flags are waving, which is impossible due to lack of air.
(at around 48 mins) When Clark tries to save Lois after she jumps into the river at Niagara Falls, he uses his heat vision to burn a branch loose while wearing his glasses. The beams burn everything they touch, yet Clark's glasses remain intact.
During the fight scene between Superman and General Zod, Ursa and Non at the Fortress of Solitude, Superman comments to Lois that he was never good at this game in school. This statement cannot be true since he left Krypton as an infant and any such activity in Smallville would have revealed his superpowers.
The Sheriff takes his hat off the dashboard and in the next shot when they see the supervillains blocking the road , he picks it up off the dashboard again .
When Superman tries to get Luthor to lure the three super villains into the molecule chamber to strip them of their powers, Luthor betrays him by telling Zod it's a trap. Luthor then tells Zod that the crystal activates the mechanism, information that he could not possibly know since Superman never told him how to operate it.
(at around 23 mins) At the prison laundry, Lex Luthor tells another prisoner he wants his Liberace record back "tonight". The prisoner responds with "There's a scratch on it." However his lip movements do not match the words spoken. In the Richard Donner cut (Superman II: The Richard Donner Cut (1980)), it is revealed the prisoner actually responded with "Tonight?'.
(at around 1h 55 mins) As Superman flies from Lois's penthouse apartment, crew members are visible inside her apartment.
(at around 50 mins) When Zod, Ursa, and Non land on Earth for the first time, Zod walks on water. In the wide-angle shot, when he walks from the middle of the lake to the shore, the outline of a board or platform is visible just under the water.
(at around 1h 6 mins) When the army enters the small town to destroy Zod, Ursa, and Non, a helicopter comes in to fire missiles at General Zod. At one point, a motion picture camera and crew members appear in the foreground, covering the action from another angle.
(at around 1h 30 mins) When Non knocks Perry out by lifting him up into the ceiling, a crew member in the lower right corner of the screen is holding Perry's hand.
(at around 1h 35 mins) During the fight in Metropolis, Ursa throws a manhole cover into Superman's chest. As he flies backwards, something is holding the manhole cover to his stomach as he bounces off the hood of a car.
(at around 1h 7 mins) When the helicopter pilot says the rockets didn't have any effect on Zod, Ursa, and Non, a policeman takes cover in front of a car. A sign on the wall behind the car says "For sale or lease, for commercial development, call 313-358-2511." Area code 313 is Detroit, Michigan, yet this scene takes place in the fictional town of East Houston in Idaho.
Superman and Lois fly to the Fortress of Solitude (which is at the North Pole). After Superman gives up his powers, they have no way to return to civilization. Somehow, they got to a diner safely which doesn't appear to be close by. (Note: it's even shown that Lex Luthor (who's human) used a snowmobile to get to the Fortress of Solitude and back).
(at around 1h 23 mins) One must wonder how mortal Clark was able to survive walking all the way back to the Fortress Of Solitude with only a lightweight jacket, slacks, and what look like wing-tipped shoes.
It is well documented that Lois loves Superman, and has no interest in Clark. But as soon as his identity is revealed to her, Clark decides to give up being Superman, to permanently become Clark.
If everyone and everything from Krypton is much stronger than anyone or anything from Earth, there should have been no way for the bomb made by the terrorists detonated in space to shatter the Phantom Zone, thus freeing Zod, Ursa, and Non.
(at around 1h 55 mins) The three villains kidnap Lois and take her to the Fortress Of Solitude in order to flush out Superman. After the villains are defeated, Lois is at the office the very next day, and still upset with the fact that she and Superman can't be a couple. You would think with the traumatic experience that Lois endured, Perry would at least allow Lois to take a personal day or two so she can recover from it.
(at around 51 mins) Zod and his gang are completely invincible to attacks such as bullets and rockets while they are on earth - they don't even flinch, yet when Ursa picks up the snake, it is able to bite her and cause her pain. (This was not even deleted/corrected for the 2006 Richard Donner cut).
All the Frenchmen speak French with each other except French Special forces who speak English with each other and with the other Frenchmen.
(at around 19 mins) When Zod, Ursa, and Non leave the Phantom Zone, they are unsurprised by their new powers (ex. the abilities to breathe in space and fly) and confused by humanity's lack of super powers. For instance, General Zod is shocked that humans cannot fly without a machine.
(at around 56 mins) The back of the sheriff's car says "COUNTY SHERIFF" but the emblem on the side says "EAST HOUSTON IDAHO POLICE". A sheriff's car wouldn't have a 'POLICE' emblem.
The three villains show that nothing can hurt or kill them, such as being hit with rockets and gunfire and not even flinching. Yet, Ursa picks up a snake that bites her, causing her pain. Later, Perry throws a metal pot at Non's head, and you can see Non flinch somewhat. Then, Lois takes a swing at Ursa, and you can somewhat see Ursa flinch.