Plot hole: When Superman becomes human for Lois, the molecule chamber nearly rips him apart, he suffers. At the end of the movie, when he tricks out of the evil 3 and turn them into humans with the same radiation, they are just looking around, wondering about the strange lights, but don't suffer at all.
Suggested correction: Well it's established that Superman has altered the machine. Maybe he also reprogrammed it to not leave signs of their powers being removed.
Continuity mistake: Under the elevator when Lois says "Nobel prize" her fingers are completely black, covered in grease. When she starts to say "lil' o" they're just slightly dirty. When Superman saves her they're spotless.
Factual error: When the police car's light is thrown at the boy and it blows up, it shouldn't have happened. The most that would've happened was that the kid would've been knocked off his bike when hit with the light. There is no explosive device in the light, so it shouldn't have exploded in the least like it did.
Plot hole: Lois Lane and other people see Clark Kent unhurt when a taxi hits him and suffers damage, but don't draw the obvious conclusion that there's something extraordinary about him.
Suggested correction: I always took this as an intentional jab at how the people of Metropolis, and Lois in particular, were so oblivious to the fact that Clark was obviously Superman. Still a plot hole, just an intentional one.
Suggested correction: Maybe the cab-driver thinks that Clark is extraordinary, but he is shocked in the first moment, worrying about his damaged car. Later than he realises that this guy is maybe Superman, but cannot find him anymore. Just a guy of millions walking around the big apple.
Revealing mistake: In closeups, you can see Lex Luthor has a bald cap on.
Suggested correction: Much too vague. What scenes are you referring to. And how can you tell, other than knowing that Gene Hackman isn't really bald?
Continuity mistake: When Zod is interviewed by the news reporter the people behind him differ or change positions between shots.
Continuity mistake: When Lois comes out of the river she turns to the left to help Clark. Shot changes and she has turned 180ยบ around.
Revealing mistake: When Superman returns the flag to the White House, not only has the shot been reused, but the trees have been badly cut around to change the previous grey sky for a bright, blue and sunny one.
Revealing mistake: When Non burns the side of the cargo bed of the truck, a rectangular spot around the planks is coloured in a lighter shade, giving away where the special FX were placed.
Revealing mistake: When the villains enter the oval office, the whole White House behind is a cheap set with painted columns, furniture, fixtures and switches (even the bullet holes are painted!). (01:16:29)
Revealing mistake: When Superman flies towards the White House, in the close-up his cape and flag flutter at a normal speed, but in the wide shot they move really fast, quite comically actually, revealing that the scene has been speeded-up.
Other mistake: When Clark and Lois return from the Fortress of Solitude in a green car, the footage is the exact same one used in Superman I when Luthor later crashed that very same car (time code for Superman I 1:34:04 vs 1:18:25 for Superman II).
Continuity mistake: While in the water, Lois grabs the log with her right hand. A shot later she is away from the log and she grabs it again, though now she uses her left hand.
Revealing mistake: When Lois jumps in the river, she is replaced by a very obvious mannequin that floats stiff. Furthermore, the current tilts the dummy and its two arms bent like a sex doll's are perfectly visible.
Continuity mistake: After Zod launches Boog through the truck the cop asks if he's OK and he and the kid turn sideways an look at him. A shot later they are facing straight.
Continuity mistake: When Zod launches Boog through the cafe window, he lands a couple meters away from the cop, but a shot later he's at his feet.
Revealing mistake: When Superman arrives at the tropical place, the sea doesn't move, revealing it's a very obvious still picture where a flying Superman has been inserted.
Revealing mistake: After the army jeep drives through a House in East Houston, notice the driver's stiffness despite the crash and fall, revealing it's a dummy.
Revealing mistake: When the 3 villains start blowing at the people in Metropolis, the papers come blowing from the left and right sides of the set, revealing where the huge fans where placed to achieve the effect.
Revealing mistake: When Ursa throws the sewer lid at Superman a sticky object protrudes from his back, revealing the mechanism that pulled him backwards.