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: 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.
Plot hole: When The Ray is injured on Earth X and has Red Tornado's cortex, he escapes by Vibe sending him into a portal to safety. However it is evident that Vibe doesn't know where he sent The Ray or where he would be going as later he's trying hard, searching the multiverse for him. Yet somehow The Ray is able to go across universes and winds up coming out right at Earth 1's Ray's feet to transfer his powers over to Ray and give him the Cortex. This makes no sense. The Ray can't control Vibe's powers or where he sends him, so he would have had no way of making himself exit the portal in Ray's back yard. And if Vibe sent him there on purpose, he wouldn't have been struggling to figure out where he went. The only way it makes sense at all is for it to be the most massive co-incidence possibly imaginable where he accidentally was sent to another universe and happen to come out right at the feet of that universe' version of himself. None of it adds up. (00:09:50 - 00:16:50)
Plot hole: When Norm is stuck under the satellite tower after disposing of the condos, he has flashbacks to numerous moments earlier on in the movie. One of the flashbacks is of Socrates saluting Norm, but the moment where Socrates salutes Norm did not occur until he was on the cargo ship being shipped off to New York and was something that he did not see Socrates do; there would be no way for Norm to have this flashback. (01:18:00)
Plot hole: Luka sneaks into Bayonetta's hotel room and plants a hidden microphone. While sneaking out, he is caught. That's when he is astonished to find a child with Bayonetta who calls her "mummy." He does eventually escape the room and sits in corner with his radio, surprised that they both went to bed and he receives nothing. The problem is: One must be an idiot to plant a mic in a lone woman's hotel room in the dead of the night, unless he truly enjoys listening to her snoring! Planting the mic in her apartment or office, or on her mobile phone makes a lot more sense.
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: When Dubois attempts to kidnap Alex using the tranquilizer, she is brought to a halt by several different zoo staff thanking her for returning him. The entire first movie's plot is based on them being stranded on Madagascar after being on a ship that was intended to take them away. The actions of the animals at the train station were on the news, and a large gathering of sorts was held to show that the animals were leaving the zoo. Therefore, no one should have reacted this way to his return.
Plot hole: If Chester's plan was to steal the machine the entire time why didn't he just have his people steal the machine while it was still floating in the air during the first film? There was plenty of time to capture it before the food started mutating so what was he waiting for if he needed it so bad?
Suggested correction: Because he wasn't there in the first film? He first made an appearance in this film, doesn't know how to work the machine without Flint, and how the hell would he even get it in the sky? He also didn't even know about it, or what happened to Chew and Swallow, again, until he made an appearance in this film. Not a mistake.
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.