Revealing mistake: After Chuck steps on the toy duck, he looks up to see the alien family and their house behind them. However, there is no reflection of this on his visor, just an empty field and the trees beyond.
Continuity mistake: As Chuck first arrives on Planet 51 he takes a few steps. The ground in front of him is clear. As he plants his flag down he steps on a duck which wasn't there before.
Continuity mistake: When Eckle's mother leaves the parking slot (after pick up Ekle from theater) there is a lamp pole that goes down (thanks to that alien dog). In next frame the lamp pole is instantly fixed.
Continuity mistake: When the movie begins, it's sunny and the sky starts to turn grey and rain stones. Immediately after, another shot of the city shows the blue sky and no traces of the grey clouds or stones on the floor are seen.
Continuity mistake: After Chuck and Lem leave the comic book store and get into the military car, at the beginning of car pursuit the "no parking" sign pole changes position between shots. First it is right beside the windows, in next shot its distance is much farther away.
Continuity mistake: The first time the spaceship touches down it becomes cloudy due to the spaceship coming into planet 51's orbit, while at the end of the movie when they escape area 9, go back into orbit and come back down to return everyone, it's nice and sunny.
Factual error: The lead song, "Lollipop," wasn't written until 1958, seven years beyond the chronological order of the movie.