During the song "The Girls of Rock and Roll," when the Chipettes sing the line "The things they're trying to sell us," their lips aren't moving at all. The same thing happens again later in the song when the Chipmunks sing the line "We'll never stop believing" without moving their lips.
While singing "Rock 'n' Roll" the Chipettes walk up some steps, and the Chipmunks do the same. Viewed from the front of the Chipmunks, the Chipmunks walk up the step in this order, from left to right: Simon, Alvin, Theodore. In the next shot, Simon and Theodore switch places.
When Dave drops the pair of mittens, Theodor has a sandwich in his hand. He picks up the mittens and calls, "Don't forget your mittens Dave; it's cold in Europe." But he clearly hands Dave the sandwich instead, and is about to take a bite out of the mittens, and then in in the next shot, Dave suddenly has the mittens.
To prove they've gone to every location, the Chipettes must drop off a Chipette doll and pick up a Chipmunk doll. However, during a musical montage, the girls are shown picking up Chipette dolls twice. Once on a windmill and then again on a ski lift when they should have been Chipmunk dolls.
In the first scene that introduces Klaus and Claudia, Claudia is wearing pink lipstick and fingernail polish. When they walk over to talk to the chipmunks and chippettes, her lipstick and nail polish are red.
Near the end of the "Getting Lucky" song, Jeanette and Brittany are both holding armfuls of Chipmunk dolls. When Eleanor enters the scene, only Brittany is holding them, and Jeanette is empty-handed. Then when Brittany is climbing down the snakes she is only holding one doll.
Throughout the movie we really only see the inside of the Chipettes balloon basket. Various times the Chipettes look too short for their heads to reach over the tops of the basket's sides, such as when they first get in the basket at the beginning of the race, and sometimes they seem to be tall enough that their heads reach over the tops, such as when they are looking for the boys after they discover the doll full of diamonds.
During the end of the "Rock and Roll" song the Chipettes are holding on to the ropes of the basket when they are dancing and they look just wide enough to fit in the amount of space between each rope. Then when they are dancing and not holding onto the ropes they look significantly smaller and appear that they would not be able to hold onto the ropes.
During the "Woolly Bully" scene the Chipmunks switch between having no dolls, having only Alvin and Brittany dolls, and having their own dolls and their counterpart Chippette dolls tied to the bottom of their stakes between shots.
During the "Boys/Girls of Rock N Roll" number, Britany moves her hips forcefully, making her skirt fly up and revealing that her panties are over her pantyhose. However, later when the chipettes march up higher stairs in the spotlight, Britany's underwear is visible again and it is now seen to appear under her pantyhose.
In Greece, the Chipmunks and Chipettes are surprised to see each other, yet they parked their balloons at the same spot. Even if one group arrived after the other, that group would have seen the balloon and known the others were already there.