When there is a lock-down in the casino, Gloria rams into the metal door and her impression appears on the smaller door. In the next scene when the black vehicle crashes in, her impression is on the bigger door.
In the casino Skipper looks through the periscope and says "I say we let it ride" and pushes the periscope up. A few seconds later the camera looks up at the chimp carrying the second chimp; and the periscope is nowhere to be seen.
US-style amber diamond-shaped traffic signs are seen in the scene, when the penguin's car crashes through the road-work-barrier in Monaco. As all European countries, Monaco uses triangular red-and-white warning signs.
When tracking down Alex, Marty, Gloria, and Melman, Dubois mentions they never should have left the forest and now they must deal with her. However, the forest is not a common habitat for any of the animals used in the film.
During the epic chase sequence in Monte Carlo, to get their Luxury Urban Assault Recreation Vehicle to go much faster, the Penguins utilize a Nuclear reactor built into the Engine with Uranium-238 powering it. Later, when they crash on the roof of the Hotel Ambassador, the L.U.A.R.V. falls and there should be a nuclear explosion as a result.
During Dubois's singing scene, she enters the hospital room that contains four lights but shoots six times leaving one on to begin her song. This is because she shoots three lights, one shot to break the glass and one to break the bulb for each of the three lights.
Considering their extreme difficulties in traveling much shorter distances unaided in the past 2 films (a problem which provides most of the series' humor), it is surprising that no explanation is given for how the animals traveled from southern Africa to Europe fairly easily.