Factual error: In the sequence where the animals get on the first subway, it says they are on the 59th St subway. But, there is no 59th St subway in NY. The only subway station close to 59 is the 57th St subway.
Suggested correction: While the other correction lists a 59th street, that's in Brooklyn. There is one in Manhattan though, 59th - Columbus Circle, which is also the south-west corner of Central Park.
Suggested correction: There is definitely a 59th street subway station: https://en.wikipedia.org/wiki/59th_Street_ (BMT_Fourth_Avenue_Line).
Continuity mistake: When Alex's crate gets knocked off the ship, there is water dripping into the crate, yet in the following shots the crate is completely dry.
Continuity mistake: At the beginning of the movie, when Marty finds the snow-bullet in Alex's mouth, he puts it in the Alex thing collection, but the collection wasn't there before and it disappears after that. (00:01:55)
Other mistake: When Alex, Marty, Gloria and Melman are talking together inside the boxes, Alex has three holes in his box allowing light in for him. Melman, Marty and Gloria have that too, but Gloria's box is lying under Alex's and Marty's, so it can't get as much light - but it does.
Suggested correction: When we see the outsides of the box on the ship we can also see little gaps caused by wood planks nailed to the sides of the box so there should be a little light coming from in between to Gloria's box holes.
Other mistake: In the scene on the boat where the mute monkey is reading the notice on the penguin's box, and signing to the other, the monkey who can speak (but not read) is translating faster than the mute monkey is signing. For instance, he states the notice says "Kenya" before the mute monkey fingerspells "Kenya".
Factual error: Hummingbirds don't live in Madagascar.
Continuity mistake: At the beginning of the second scene, you can see a man with a camera filming the penguins, but when one penguin says, "Smile and wave," the camera man has disappeared. (00:05:20)
Continuity mistake: When Alex runs angrily after Marty on the beach, the footprints on the sand disappear faster than they should.
Continuity mistake: When Marty opens the thermometer from Melman, he puts it in his mouth and then spits it out, but it then disappears. (00:08:55)
Continuity mistake: When Alex tries to get Melman out, he is lying near the sea, but when Alex tries to get him out with the tree, he is farther away from the sea.
Continuity mistake: The HELP sign Alex changes to HELL disappears when he goes to Marty's side.
Factual error: A ship of that size would not list like that when turned as it did. It would take a huge turning circle and not list. (00:27:00)
Audio problem: Near the beginning, when the two metal monkeys strike the Central Park Zoo bell, it makes two different tones. As it's the same bell they're hitting, and they hit it at the very same vertical axis, it should make the same tone both times.
Continuity mistake: The giraffe is being transported in a crate which says 'Giraffe' with an arrow pointing to it in order that people know which way is 'up'. This piece is later used as a makeshift headstone for the Giraffe's 'protest' grave on Madagascar. On this piece the arrow is now pointing away from the name towards the grave, in other words on the crate the word would now have been displayed upside down.
