Other mistake: When Leela is signing the petition, Amy grows a third arm for a split second.
Other mistake: When Skinner calls his lawyer he never dials the phone.
Other mistake: After all the plants have stopped being pollenated when the pollen jocks are getting ready for liftoff you see the branches outside the window have green leaves.
Other mistake: When Homer drives through the barrier the second time (leaving the lake after dumping the silo) pay very close attention, his car smashes one portion of the barrier, but his car passes through a second portion of the barrier without breaking it. (00:23:50)
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.
Other mistake: Before Lex can shoot Lois and Jimmy, Dark Superman suddenly shows up and cuts through his gun with his heat vision. The laser goes right through the gun, and Dark Superman made it powerful enough to cut through the metal of the gun. Yet the next shot shows Lex standing right next to a glass incubation chamber for a Superman clone, and there is no damage to the chamber at all, or the floor, or any evidence at all of the laser. (00:58:20)
Other mistake: Whenever the fire scene is going in slow motion, the fire in the background is not in slow motion. (01:07:00)