When the crates are stacked on the boat, Melman's crate is big enough for him to move around in. However, when Alex is trying to help him out of it, it is obviously smaller, and Melman cannot even get out of it.
When Skipper asks the talking chimp if he can read, he says that he can't read but Phil can. Earlier on in the film, the talking chimp takes what appears to be a newspaper from a trash can and starts reading it.
The interior size of Alex's crate varies from when they are stacked on the ship to when he is on the ocean sleeping.
When towards the end Marty shows his butt to explain how he knows how much of a pain in the butt Alex is, it is the wrong side of his butt.
When Gloria kicks out the bottom of her crate to send Alex flying, Alex lands on top of Melman even though he was not only headed in an entirely different direction but also would have overshot Melman by quite a bit anyway.
In this film, pineapples grow on trees in the jungle. In reality, pineapples grow on the ground.
Since the penguins joined the mammals when they were busted at Grand Central, it is safe to assume they didn't sneak onto the ship but were put there on purpose to suffer the same fate as the mammals. However, a reporter claims that all the busted animals are being sent back to their natural habitat even though there are no wild penguins in Kenya.
The orientation of the word 'GIRAFFE' on Melman's crate changes when he uses it for a tombstone (from parallel to the arrow to perpendicular). However, if you look closely earlier in the movie, you can see in certain shots that the other side of the crate has 'GIRAFFE' perpendicular.
Real lemur tribes have a matriarchal structure and not a patriarchal one. The female lemurs are the ones who lead the tribes and do most of the fighting. Instead of King Julien it should be Queen Julianna. However, his right-hand man did say he was the self-proclaimed king of the lemurs, so he likely rules in name only.
"Fossa" is pronounced "foosa" in some parts of Madagascar.
The crates are stacked on the deck with Gloria's crate at the bottom. The crates all appear to be of the same depth, and when seen from outside they appear to be stacked neatly, but there's still light coming into Gloria's crate from the hole in the top even though the hole should be covered by one of the crates stacked on top of hers. However, this was so that we would be able to see Gloria in her crate and not be staring at darkness (the same would have applied otherwise to Melman's crate as it was upside down.)
Mason refers to Phil as a "filthy monkey." Although chimps are apes and not monkeys, Mason clearly meant it as an insult.
Right after the cop asks if he can shoot the zebra, before Marty can cross the street, his left front leg goes crazy for 2 seconds.
On the boat when Phil the chimp is telling the penguins "Ship to Kenya wildlife preserve, Africa" in sign language, the other chimp says Kenya before Phil signs it.
When Gloria, Alex and Marty are in the ship containers and are having a conversation, Marty and Alex's crates are on top of Glorias- yet there is still light being let through.
The animals take a subway from Central Park to Grand Central Terminal. They are seen on a subway platform on 59th Street and Lexington Avenue, which is the correct subway station that you would take from the south end of east Central Park. However, on the platform, the sign shows that that platform is for the 4, 5, and 6 trains. In reality, the 4 and 5 trains are express trains, and stop at express platforms underneath both the local platforms and a platform for the BMT Broadway Line. So except for during service disruptions, the 4, 5 and 6 would not all stop at the same platform (though late at night, 4 trains run local and use the local platforms). Also, the train is shown to be one of R62 stock cars. However, this stock has two sets of doors on each side of the car. In reality, IRT rolling stock has three doors on each side.
When the animals have fallen off the ship, the crates go underwater. You expect that the crates will be filled with water, but they are completely dry.
When on the ship, the penguins peep out of their crate through circular holes that are clearly big enough to let them out, especially for Kowalksi and Rico. There was no need for Rico to break them open with a fake key.
Private cannot read, but when the computer displays the message that he overrode the system he somehow knows that this is the message they need even though it could just as well have been an error message as far as he could know.
In real life, lions, zebras, giraffes, and hippos don't live in the Central Park Zoo.
Here's the thing. When Alex, Gloria and Melman got to the train station heading Central Station, when they enter the train, we can see Melman's tail glitching on top of the roof of the train going inside.