Continuity mistake: When Alex was a baby and was put on the Zoo rock, for a few seconds his head has leopard spots on it. (00:04:55)
Continuity mistake: At the end of the movie, it's revealed how Alex can tell Marty apart from all of the other Zebras - when Marty walks away from the "camera" it shows the huge bite mark on his backside that Alex gave him in the first movie. However, the bite mark is never seen in any other shots of Marty's backside throughout the film.
Continuity mistake: The mark on Alex's paw disappears when it shows him for the first time as an adult at New York.
Suggested correction: The mark is actually right there on his right paw. Check it.
Continuity mistake: When the penguins are hijacking the jeep, the guide jumps from the driver's seat with nothing in his hands and never returns to the vehicle before the penguins drive away with it. Yet, somehow, he has his rifle over his shoulder as they drive away.