Continuity: WALL•E first presents the plant to EVE while facing her directly. Later, when EVE replays the same scene in the Captain's quarters, WALL•E is shown holding the plant from a 3/4 profile.
Continuity: EVE's facial dirt markings disappear and re-appear. EVE gets several dirty markings on her otherwise pristine white exterior while in the garbage hold. A long dark stain runs down the right side (her left) of her "eye screen". When she flies WALL-E and M-O out of the garbage hold into the corridor, and is photographed aiming her weapon at the steward robot, and in shot when locking the steward away, the marking is clearly gone. Immediately after, as she is flying down the corridor, followed by a growing group of faulty robots, the mark reappears. During the battle with the large contingent of steward robots, in the beginning when she shoots a steward, the mark is gone, but as she shields herself when the 'massage' robot is let loose, the mark reappears.
Revealing mistakes: When the spacecraft carrying the EVE units docks inside the Axiom, among the robotic arms that attach to the ship is a two-conductor device resembling a heavy-duty power connector. Just after it connects to the ship, several small, black marks appear around it for one or two frames. They appear to be rendering errors on the part of the animators.
Factual errors: When AUTO causes the Axiom to tilt during his fight with the Captain, everyone and everything slides down the floor toward the side of the ship. In space, away from a planet, there is no gravity; therefore, there must be some type of gravity generator keeping everyone on the decks of the ship. Merely tilting the ship would not cause everyone to slide to one side - the generators would still pull toward the floor. AUTO could have adjusted the gravity generators in such a way to cause everything to slide to one side, but there would have been no need to tilt the ship.
Incorrectly regarded as goofs: In the video of the president of Buy N Large (Shelby Forthright) saying the Earth is contaminated, the president himself is a live action person (Fred Willard). In the rest of the movie, the people are represented in CGI form. This was an intentional stylistic choice made by the film makers.
Continuity: In the scene where WALL·E first meets M-O, The cleaner bot, the tread marks WALL·E makes on the floor don't match his treads - they're pointing the wrong way.
Miscellaneous: EVE is an acronym for Extraterrestrial Vegetation Evaluator, yet she is not looking for vegetation extra-terrestrially, she is looking terrestrially for vegetation. But the movie would not have made sense with an 'TVE' probe.
Factual errors: While WALL·E is traveling in outer space, the stars in the background are blinking as we would see them do on a starry night. In reality, the apparent blinking is due to the atmosphere between the star and the observer, so in space this phenomenon would not occur.
Revealing mistakes: In the animated short BURN.E, when the robot is waiting for the doors to open the light can be seen dimming to show time is passing. But, the AXIOM is not in orbit. Inside the time of the day is controlled by the captain.
Factual errors: In the video explaining the effect of being in space for long durations, the narrator points out that there would have been significant bone loss. However, it is shown throughout the movie (particularly when EVE and WALL·E are in the garbage airlock) that there is an artificial gravity simulator built into the ship which should have reduced or eliminated any bone loss.
Miscellaneous: During the scenes when the captain is about to wake up and when he confronts the auto-pilot about the plant. There is a shot of all the previous captains of the ship. A careful inspection of their ages reveals all of them lived well above 100 years and some of them even lived for 140+ years (with poor diets and lack of exercise).