Revealing mistake: When Alex says they should go find the penguins, he says "To home" and Marty, Melman, Gloria and Julien place their hands on top of his hand. In the next shot it shows all of them together. But due to the position of Julien and his arm length, it would have been impossible for Julien to have his hand fully placed on Alex's hand. (00:05:05)
Factual error: After Captain Dubois escapes from jail, she looks up missing lion on a computer and finds a news page with Alex on saying "FAMOUS CENTRAL PARK ZOO LION MISSING" and hits the Print Screen button on the computer and the news page prints. However, pushing the Print Screen button wouldn't print a document. It would just take a copy of the screen. No matter how much you push the Print Screen button, the page wouldn't print off. (00:40:20)
Other mistake: In the scene where Vitaly jumps the flaming hoop again, in the shot before he says to light the hoop on fire, if you look at the dogs you can see that three of them do not look like they do in the rest of the movie. One of them even looks completely different.
Factual error: When Alex, Marty, Melman and Gloria emerge from the water at Port De Monte Carlo, the snorkels they used to breath in were under the water. They could not have been able to breath if the snorkels were in the water. (00:05:50)
Deliberate mistake: When Julien is about to pull the switch to turn the power off in the Monte Carlo casino, the sign above the switch says "LE POWER." Monte Carlo is in Monaco, where the language is French, so the sign should be in French. Obviously "THE" is in French as "LE." But "POWER" is not in French. The sign should have said "LE POUVOIR." (00:10:15)
Continuity mistake: When Alex wakes up after having his nightmare about everyone becoming elderly, his eyes are blue. In the next shot, his eyes are green. (00:01:55)
Continuity mistake: In the shot before Vitaly starts the new show, there are only five dogs when there should be six. (01:04:15)
Audio problem: During the escape from Monte Carlo they all drive a van off a roof to land on the roof of the Hotel Ambassador. Captain DuBois drives her bike of the same roof to catch them. While she is in airborne she jumps off her bike onto the roof of the Hotel Ambassador and the bike falls to the ground. Yet we don't even hear the bike landing on the ground at no point despite the fall only taking a few moments. (00:17:35)
Factual error: During the casino scene, we see a roulette hand and the ball is landing on 36 black. In real roulette games, 36 is always red.
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.
