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)
Plot hole: The newspaper headline showing young Alex being rescued from a crate is dated April 8, 1972. In the next scene, we see young Alex dancing in the Central Park Zoo, and watching him are Marty, Melman and Gloria as baby animals. This makes no sense at all. In the first film, Marty celebrates his tenth birthday. Key word: tenth. It is also known that the scenes of the main characters as adults take place in the present i.e. Alex confessing to breaking Marty's iPod. Seeing how the animals age quicker than humans, Marty, let alone his three friends, would have to have been born in the mid-1990s and the flashback scenes could not have taken place in 1972.
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.
Factual error: When Moto Moto and Gloria were digging for water, they threw all the jewels and gold into a pile. The gold in the basket would weigh more than 1200 pounds. Also, real gold comes fused to other rock and rarely in pure form.
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.
Other mistake: Judging the angle Teetsi leaps towards Alex at, there is no way that he would hit him in the eye.
Factual error: When young Alex is in the crate, he floats from Africa to New York, dead against all prevailing currents.
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.
Other mistake: When the plane is crashing the two parachutes are deployed at the front of the plane yet the plane remains level when landing.