Continuity mistake: When Wall-E presents Eve with the plant, he is facing her directly. When Eve is later viewing the footage from her security camera, Wall-E is shown facing at an angle towards the left of the screen, instead of straight ahead.
Factual error: 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, despite that trash having been compacted. 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 densely compacted cube.
Continuity mistake: In the final scene on the lido deck when Auto alters the ship's gravity the people mover falls off it's tracks and barrels towards the passengers, smashing a huge path through the hover chairs. When normal gravity is restored and they hyperjump to earth most of the chairs are back in place.
Continuity mistake: When EVE is heading to the holo-detector with Wall-E and MO, Auto tilts the ship/alters the gravity field so that everyone on board (basically the entire human race) slides across the lido deck and piles up on the starboard bulkhead. When Captain McCrea takes control and rights the ship everyone is still piled against the bulkhead, with just a few people falling off the pile and some attempting to walk for the first time. Five seconds later when tossing the plant to EVE and going into hyper jump everyone on the ship is now equally distributed across the entire lido deck area.
Continuity mistake: The sky over Wall-E's city is totally covered, from horizon to horizon, with thick brown clouds. When the Earth is seen from space at the beginning of the film, there is no such cloud cover anywhere on the planet. It looks more like the old Universal Studios logo than the actual Earth. The clouds appear out of nowhere as the camera zooms down.