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.
When Superman takes Lois flying for the last time, scenes from Superman 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.
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.
After Clark is beaten up in the diner after giving up his powers, and realizes Zod, Ursa, and Non are wreaking havoc on Earth, Lois tries to console him by saying "You didn't know." Clark responds, "He knew." He was referring to his father, whose scenes were filmed with Marlon Brando before they were cut. In the film that was released, Superman's mother tried to convince him to keep his powers.
During the confrontation between Zod, Ursa, and Non, and the sheriff and the deputy, a wide shot clearly shows the villains standing on the dirt road, with a huge hill full of trees behind them in the background. Before and after that shot, the horizon behind them is empty, except for some bushes and a few trees.
When Zod, Ursa, and Non leave the Daily Planet offices to chase Superman, all three of them fly out of separate windows, and only those windows break. After the shot of a bunch of debris falling to the sidewalk, and the whole wall of Perry White's office is gone.
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.
When Lois climbs onto the undercarriage of the elevator, she is laying on her stomach. When there is a close up of the Eiffel Tower model with the elevator going up, you can see the doll used to represent Lois Lane is lying on its back, with its arms up, holding the underside of the elevator.
After Superman catches the people in the bus, General Zod blows wind at the people in the street that come after him. The people in the street are blown backward along with vehicles and debris, but the flames are not effected at all.
Just before Superman sets the antenna back on top of the Empire State building, the area where the antenna tore away from the mount is rough and sparking. When he sets it on Non, the mounting surface is completely smooth.
When Rocky takes Clark's seat in the diner, the man behind the counter brings Lois's Coke while pouring it into the glass. In the next shot, the can and glass are on the counter and the man is gone. In the shot after that, the man is back again, still pouring it, and then puts it down for Lois.
Superman and the three super villains are battling it out over several square miles above Metropolis, yet, Lois Lane should not be able to see them from that distance as she watches from the Daily Planet Building, as she reacts to her co-workers that "the bigger one [villain] is just as strong as Superman."
When Superman flies past the camera at the end, before the credits start rolling, he raises his left arm. Something square sticks out, stretching the fabric of his suit. It's part of the rigging used in the front projection process.
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.
During the big confrontation between Superman and the villains in Metropolis, he is shown flying above the water around the city, and the wake left by the boat used to film the background is visible in the lower right part of the screen.
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.
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 Houston, Idaho. Commercial developers sometimes deal with properties outside their home cities, but Houston appears too small for a Detroit-based developer to have any interest in commercial development there.
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.
The police car in East Houston, Idaho says "Police, East Houston, Idaho" on the side, and "County Sheriff" on the rear. The officers' shoulder flashes indicate that they are sheriffs and deputies. In the U.S., sheriffs and deputies are peace officers with police powers at the county level. Their vehicles do not say "police" or the name of a town. Those would be on a municipal police vehicle, whose members would not have shoulder flashes or markings referring to sheriffs.
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.
During the fight in Metropolis, Ursa and Non throw a bus at Superman. On the bus is written the word, 'Theatre' (amongst others). Since the scene is in America, the word should be written, 'Theater'. The film was mainly shot in the UK.
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, and he appears in Metropolis for the showdown with Zod, Ursa, and Non as if it never happened. In the Richard Donner cut, Jor-El gives his remaining energy to Superman so he can recover his powers.
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 battle in Metropolis, when Zod is getting ready to hurl a slab of concrete at Superman, the view of the crowd is shown reversed (note the "No Entry" sign). It is corrected in the Richard Donner cut. 'Superman II (2006) (V)'.
After the scene at the Daily Planet, Zod, Ursa, and Non fly through editor Perry White's window. In the first cut, the window is open and there is no glass. In the second cut, seen from the outside, glass appears as through they've flown through a closed window.
While flying away from the moon after the confrontation with the astronauts, Non throws the American flag and pole into the moon buggy. It drops normally, and not more slowly as it would in the Moon's reduced gravity.
When Lois and Clark are driving from the Fortress of Solitude after Superman gives up his powers, the car is actually from Superman. 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.
When Lex Luthor and Otis talk in prison, Lex Luthor's bald head is obviously a bald cap. The flaps meant to cover Gene Hackman's sideburns are visible, and when he faces the prison wall during his escape, the back part on his neck wrinkles like a plastic cap would.
When Zod, Ursa, and Non are blowing people and cars all over the place, several little dolls are being pulled along a track on the model sidewalks, in front of the buildings, to represent the people being blown down the street. A few model cars slam directly into the dolls, and they pop right back up.
When Lois and Superman are flying to the Fortress of Solitude after she discovers his secret identity, the scaffolding used to hold her and Superman is visible. A big square piece is pinching the material of her dress together on her right side, by her waist.
When Superman is converted to an ordinary mortal, he undergoes a seemingly painful and visually obvious transformation. Later, when Zod, Ursa, and Non are tricked into losing their powers, they are completely unaware the same process is occurring.