Continuity mistake: Clark runs towards the subway train and stops. Then from a different angle he is several meters behind, running and stopping again.
Sacha
Continuity mistake: The smoke coming out of the volcano changes direction in a split second after nuclear Man enters the crater.
Sacha
Continuity mistake: In the quarry, Lenny parks his car to the very right of two wagons. Seconds later the car is in front of them.
Sacha
Continuity mistake: When Superman is rebuilding the Great Wall all of the people near the hole vanish.
Sacha
Continuity mistake: When nuclear Man makes the engine of the taxi explode, there's a guy with a red jacket behind it that appears and disappears between shots.
Sacha
Continuity mistake: Swat agents hide behind the van and start to shoot. A second later they've all vanished.
Sacha
Plot hole: Superman dropping Nuclear Man in the area of a nuclear plant would have made him stronger, since that is giving him a lot of nuclear energy. Instead he is killed.
Athletic JasonSuggested correction: Dropping nuclear man in to a nuclear power plant isn't as silly as it seems, assuming that the nuclear power is far greater than nuclear man he would simply be absorbed by it rather than growing stronger.
That never got shown and the fact that he was able to make a volcano erupt speaks volumes.
Athletic JasonContinuity mistake: Superman walks towards the UN and there are benches in front of him. In the next wide angle they've disappeared.
Sacha
Continuity mistake: When the train driver passes out, several (speeded-up) shots of the tunnel and the shots of the bystanders on the platform show that the train is moving really fast, but in between there's a shot of Lois at normal speed, and the lights of the tunnel seen through the windows show that the train speed is quite low.
Sacha
Continuity mistake: When Nuclear Man destroys Metropolis, he stands by the Metropolis Tower entrance, but disappears and reappears randomly depending on the angle.
Sacha
Continuity mistake: During the subway sequence, the carriage in front of Lois's is empty, but when the train comes to a stop it's packed with people.
Sacha
Continuity mistake: When Clark is about to leave the hotel, a man appears by the dark car on the right in less than half a second.
Sacha
Continuity mistake: When the bellboy picks up Clark with the baggage trolley, he makes a close turn to the right and drives parallel to the elevator. When the angle changes he is in a totally different position.
Sacha
Plot hole: Superman manages to find bricks to rebuild the Great Wall of China. While it's true that he could have created the bricks from stones, the humongous explosions of the wall, and the vast grounds surrounding the area, show that there is no place, no material, and no way even for Superman to create 1,000 bricks from nothing.
Sacha
Continuity mistake: One of the general shots in the subway shows Superman flying slower than usual and inches away from the bystanders. The problem is that their coats and hair don't flutter nor do they notice him passing by or seem nervous in any way. However, the next close shot of their faces show them nervous and in awe at the action.
Sacha

Continuity mistake: On the moon, nuclear Man grabs a rock with a huge hole underneath and holds it over his head. The angle changes and the rock has changed to a different one with a solid bottom.
Sacha
Revealing mistake: When Lois and Superman are flying together, they turn green, specially Lois's arms and hands.
Sacha
Continuity mistake: After Perry White delivers his final speech a woman in a yellow dress goes up the escalator. In the following shot, no one's there.
Sacha
Continuity mistake: While Nuclear Man is destroying Metropolis, two police cars get moved backwards. The first shot of the cars moving show a lot of people by a shop window. The angle changes to a close shot, with no people there, then back to the previous wide angle, now with the cars moving backwards, and the bunch of people reappear.
Sacha