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: After Lady X is taken away, the doctor arrives with an antidote that can bring the Ikes back to life, which he then gives to Polar Penguin who is just sitting in a Copa-Banana chair in the middle of the street. What exactly was Polar's dead body doing there? Last time he was seen, he was at the Copa-Banana and had died from his injuries, but his body is shown sitting in a chair in the middle of the street. The doctor creating an antidote that would undo his injuries was completely unplanned, so there is no real reason for his body to be out in the middle of the street like this. (01:20:45)
Plot hole: Throughout the movie, Bladebeak works for the villains. But, during the climax, he becomes a good guy without any explanation.
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: 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 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: 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.
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.