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: Close to the end of the movie when Sykes is chasing Fagin on the train tracks Jenny says Fagin's name. Fagin also seems to know Jenny's name as well because he says her name and tells her to jump. How did they know each other's names?
Plot hole: When Wilbur and Lewis are time traveling for the first time, Lewis says he's done with the memory scanner. Since he said he wouldn't invent Dor-15, and she went away, wouldn't the time machine and everything else in the future go away since the memory scanner started it all and Lewis decided to quit?
Suggested correction: Lewis wasn't fully giving up. He was just frustrated and probably went back to it later anyway. Whereas with Doris, he deliberately decided not to invent her because of the danger she posed.
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: 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: According to the phone book the name given was "M. Horowitz" but when Mary mails he first letter to him she already knows it's "Max."
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.
Plot hole: Cruise leaves Lugnut to go buy he and Coupe some seats and mere seconds after leaving, Coupe appears in the scene and talks with Lugnut. Coupe asks if he has seen Cruise, but even if Cruise had already left to go buy tickets, Coupe would have already seen him when approaching Lugnut since she only arrived seconds after he left. (00:09:15)
Plot hole: Alberto didn't sign up for the Portorosso Cup, and he enters anyway. This should've gotten Luca disqualified.
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: Rafe is not a supernatural being, and besides not suffering any fatigue at all missing his sleep to do his pranks, some are outright impossible to execute and perform overnight for a person of his age (most likely for an adult in their prime too). Covering the entire hall and corridors, plus the principal's office, with post-it stickers requires a ridiculous amount of stickers to begin with, and arranging them creatively covering the whole walls, floor to ceiling, so that they create drawings, is an insane concept. Even more insane when it's the opening prank, anything he does later in the movie including the big movie finale requires less labor and time than his first act did.