Plot hole: It's one thing to have a small amount of liquid nitrogen (about the size of a standard propane tank, by the looks of it from the Fridge scene), but where did the gallons upon gallons of it during the climactic flood scene come from?
Plot hole: At the end, none of the duplicate Benders that are waiting in the limestone cavern under the Planet Express building have had their Obedience Virus or the time code deleted from them. There should have been only one Bender without the Obedience Virus, not all of them.
Plot hole: In the scene where the Sheriff stops the cows' brawl, he gives them to the Chinese man. The Sheriff knows what Pearl's animals look like, so why didn't he recognize the cows as Pearl's?
Plot hole: Throughout the movie, Bladebeak works for the villains. But, during the climax, he becomes a good guy without any explanation.
Plot hole: When Dex is rescuing the baby kittens from the Fat Cat Burglar on the hot air balloon, whilst it is flying over the city, the four hairless hamster henchmen fly off the balloon and plummet down onto the street. Dex then saves the baby kittens and lands in the park, where two of the henchmen are shown landing in the park after plummeting. Three problems with this. 1) The henchmen fell before Dex saved the kittens and made his way down to the park, so how did they land on the ground long after Dex landed on the ground? 2) How did they land in the park if they plummeted from above a street? 3) How are there only two henchmen shown landing when four of them were shown falling all at once? (00:04:30)
Plot hole: When Sully and Mike are talking in the toilets, during Boo and Sully's Hide and Seek game, Boo comes running in screaming and upset because she's just seen Randall, and he's not too far behind since all three can hear him talking offscreen to the CDA before entering the toilets, but how did Boo get to Sully faster than Randall without him seeing her, and how did Randall not hear her screams since they're all in the changing rooms which have an echo?
Plot hole: During the climax with Van Helsing and the Kraken the writers of the film seemed to have forgotten about the powers Dracula has always had. At no point does his super speed or indestructibility ever come into play, he could have easily climbed up to the DJ booth and dealt with Van Helsing in seconds instead of going through the silly DJ battle.
Suggested correction: The kraken was faster and stronger than Dracula, if you watched he kept trying to reach the DJ booth and fight but was stopped each time and nearly crushed. It was said that the kraken was extremely strong and the only thing that could subdue him was a more powerful song than the other.
Plot hole: When Quasimodo is revealed to the crowd during the Festival of Fools, someone identifies him as "the bell-ringer from Notre Dame." This is the first time Quasimodo has ever left the cathedral, so he shouldn't know that.
Plot hole: Why is that shark machine even there? The only reason it's there is to help the plot, and I don't see how it is of use to anyone in the corporate world. If the shark just ejects the fish it turns into fish heads out to sea, there is too much chance they will be ruined by carnivorous fish or weather before they are picked up. And fishing companies should know better.
Plot hole: Even if Chicken Little was tagged out when he hit home plate, the game was already tied so his team would still have a chance to win the pennant.
Plot hole: There are two cars driving behind the EPA truck containing Marge, Bart, Lisa and Maggie. When Homer uses the bulldozer to try and break the family out of the truck, the two cars behind the truck don't notice the bulldozer trying to destroy the truck. There's no way they couldn't have not seen the bulldozer since they were just behind it. (01:00:05 - 01:00:40)
Plot hole: I can somewhat understand that in a kiddies' show all aliens can inexplicably speak English - but using Terranean (i.e.: Arabian) numbers as well? While Tetrax's computer uses alien runes, the readout on Gluto's holographic HUDs use Arabic numbers - somewhat a bit too deliberate a producer choice to emphasize intergalactic communication.