Continuity: The birthmark on Alex's paw appears and disappears between shots.
Anachronisms: The newspaper headline showing Alex being rescued from his crate is dated 'April 8, 1972', yet World Trade Center 2 was not completed until 1973. This would also put Alex's current age at around 36.
Continuity: There is a shot in which the monkey is cutting through the middle frame with a grinder, then in the next shot he actually completes the task on the rear one.
Continuity: In the very end of the movie, Alex glances at Marty's butt, which has a bite mark supposedly made by Alex from the first movie. However, the mark cannot be seen in any other scene that shows Marty's butt, such as the very first one when they are all shaking their butts with the music.
Continuity: In fight between the old lady an Alex on the African road, at the end, we see a shot of the bus directly behind them, but after the fight, the old lady walks quite a ways to get to the bus.
Plot holes: At the beginning of first Madagascar film, Marty celebrates his 10th birthday, which would put his birth year at late 1990s. However, in Madagascar 2 it is shown that Marty is already at the Central Park Zoo (as a cub) when Alex arrives, which happens in 1972.
Continuity: In the scene where the penguins steal the tour jeep, the tour guide has no gun yet he has one when the humans pick up the old lady after the penguins leave with the jeep.
Continuity: When they ram the dam you can clearly see the old lady purse fly into the water and go down with the dam but they later give it to Makunga.
Continuity: At the beginning of the film when the zoo-keeper places Alex on the newspapers on top of a stone table where Alex performs, the newspaper disappears moments later.
Continuity: The birth mark on Alex's paw is never seen in the first movie.
Incorrectly regarded as goofs: The title, "Madagascar: Escape 2 Africa," might appear to be misleading since Madagascar can be considered part of the African continent. However, whether Madagascar is strictly part of Africa is perhaps geographically debatable, and certainly politically debatable. Technically, Madagascar is an island east of Africa. Politically, there is no pan-African government, and attempts to have Madagascar integrated into the African Union have historically been abortive. Furthermore, considering the various botched plans involved in the plot, the filmmakers undoubtedly intended the subtitle "Escape 2 Africa" to be somewhat ironic.