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.
Revealing mistake: When Ursa kicks the astronaut into space, she takes a step back and looks upwards. When this happens you can tell that the film is being shown at double speed. Also, when Clark spins the guy on the chair at the end of the film, he snaps back upright far too quickly.
Continuity mistake: When Zod throws the shotgun after discharging it, it lands in front of the police car's back tyre. But when the dumb one goes to pick the gun up, it is now towards the back of the car.
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.