Continuity: When EVE is reactivated on the Axiom bridge, she 'sits up' on her transport bed. The camera shot changes and she's 'standing' well in front of the bed rather than on it or even right next to it.

Other: In the life pod scene, GO-4 puts the plant in the middle of the pod. Just before this Wall-E and Eve peer around to see it doing so. If you look very quickly at Eve's back when the camera pans around, you can see two different textures flick on and off. This must be an animation error.

Plot hole: As a trash compactor Wall-E does not function logically. When he fills his chest compartment with garbage and runs his internal compactor, the cube that exits his body is the same volume as the trash he puts in. He does not add extra trash to fill the empty space after running the compactor - there are three scenes that show him filling up only once with loose garbage and then ejecting a compacted cube.