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.
Suggested correction: Just because it appears dry on the surface doesn't mean there isn't water between the slats of wood making it drip.
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)
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.
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.