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".
Deliberate 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.
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.