Audio problem: At the scene where Mikey asks the elder penguin if anyone surfs in Shiverpool, when he says,"You know you're standing on thin ice," his beak never moves.
Other mistake: Right at the beginning of the movie, when Lewis's real mum picks him up from the box and hugs him, it's no more than three seconds before she hears Lewis from the future slipping on the step. She gets scared and puts baby Lewis back in the box. When Wilbur takes Lewis to meet his mum, near the end of the movie, the time his mum holds the baby is more than twenty five seconds.
Continuity mistake: While discussing her bodily changes during adolescence, Marji says her left foot became enormous, but the scene shows her right foot growing larger.
Continuity mistake: When Abe is being tortured by the Harpies, at one point, you can see that his body is covered with cuts and his blue-colored blood. The blood then disappears and reappears in subsequent shots.
Continuity mistake: When Doomsday slams Superman down into the subway, the hole they make in the street is right in the middle of a crossing. But a minute later in the film as civilians are walking up to the hole, there are no lines anywhere around it. Moments later after Jimmy takes a picture of the hole, the shot cuts to a far angle and now the hole is next to the crosswalk lines, and in that shot the stairway entrance to the subway station also vanishes. The road also becomes much wider with more lanes, and the red truck turns around. (00:22:40 - 00:23:25)
Character mistake: When the Level 3 Sentry gun is revealed on the right of the screen and fires a rocket barrage to the left, you hear it explode as the Engi looks over. You then hear Scout scream "My arm!" really loud. Then an disembodied arm falls in front of Engi with a plop. However, this arm is from the character model of Sniper, not Scout. (00:00:45)