When the penguins are trying to rescue the egg, both the snowball that the egg was in and and the snowball that the penguins were in disappear by the time the seals attack them.
When the North Wind brings the Penguins to their headquarters, Classified is seen with a cup of Espresso. But after the Penguins finish playing with the chairs, Classified is now holding a pen.
At many points in the film the penguins change positions when the camera angle changes.
After the boat explodes at the beginning of the movie, no evidence of this explosion is visible just seconds later.
When the baby Penguins are trying to rescue the egg, both the Penguins and the egg fall down the same path and then fall when the same snowbank breaks off. But the snowbank shouldn't even be there for the Penguins to land on in the first place.
Whenever Dr. Octavius Brine/Dave is around humans, he uses a translator-like microphone that helps him speak to them. But during the mutant penguin invasion, he shouts "Somebody call the exterminators!" and doesn't use his microphone and yet the humans understand him. It is possible that sometimes in the Madagascar films, the humans can understand the animals and sometimes, they don't.
During the chase scene between the penguins and the three octopus, the octopus trio row on one side of the gondola, this would have caused the gondola to go in circles, not forward.
In the BBC One print, instead of the correct 20th Century Fox logo, the Paramount Pictures logo is shown, even though DreamWorks Animation leaves Paramount for 20th Century Fox as distributor in 2012.
Venice has no roads for automobiles. The truck loaded with watermelons would not be in a city accessible only by boat or foot.
In Dave's back story, the zoo octopuses need to be in ocean water as in real life. No explanation is given for why the octopuses in the main story can breathe air and live on dry land, which should be an important plot point.
At the end of the movie, Skipper, Kowalski, and Rico turned Private back to normal on Thursday. However, Skipper told Private that they were going to turn him back to normal on Monday.
King Julien uses the same crown from the first film and the TV shows he gave the crown to Alex but he wears it in the end of this film.