Factual error: In the final surfing scene, Cody and Z are surfing, presumably, off into the sunset. However, being on the north shore (given Z's remark a few moments before), that would mean the wave is rolling to the south which would put the sun toward the east not the west. (01:20:00)
Factual error: When Wilbur tosses Lewis onto the time machine, he should have broken or hit the glass covering the back half. And he is on all fours when the machine becomes visible, which shows he would have had his face hitting the driver seat, yet he scrambles back into the passenger seat without a problem, then is seen barely leaning forward to talk to Wilbur in the future.
Factual error: After dealing with the workers in the tunnel, Doomsday gets to the surface, kills all the Applecore workers and destroys their equipment and vehicles. Fires are everywhere from explosions and men scream as Doomsday crushes them. Once he finishes off the last guy, he walks a few steps away from the destruction and sees a deer just haplessly grazing on some grass nearby, only a few yards away from the Project Applecore. Only when the deer sees Doomsday does it decide to stop eating and take off running. Deer are afraid of loud noise. The explosions and men screaming only a few yards away would realistically have spooked that deer and just about any other wildlife in the area to run away. (00:11:15)
Factual error: In the scene where the angry mob is attacking the Simpsons in the tree house, Grandpa Simpson is shown aiming a double-barrel shotgun, which he then pumps to ready it for firing. There's no such thing as a double-barrel pump-action shotgun. (00:36:20)
Factual error: When the Level 2 Sentry gun begins firing, you can see Shotgun shells falling out of it instead of the usual ammo casings. (00:00:40)
Factual error: Remy sniffs the messed-up soup and almost throws up. Rats can't retch.