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.
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.
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.
Continuity: When WALL·E first adds the Zippo lighter to his collection, he very carefully places it in the lighter bin facing out. When he first rotates the junk bin after he meets EVE, the lighter is gone. It returns again when EVE goes to pick it up.
Incorrectly regarded as goofs: In the film, WALL·E collides with Sputnik 1 (the first man-made satellite) during the liftoff of EVE's spacecraft. However, the real Sputnik 1 burned up in Earth's atmosphere in 1958, so WALL·E couldn't have possibly hit it. The filmmakers almost certainly knew this and included it anyway as an incidental visual joke.
Factual errors: The probe has to penetrate a shroud of satellites supposedly still in orbit after 700 years of disuse. But even geostationary satellites will either re-enter or fly off after ~300 years, and many of the satellites pictured are low-Earth-orbit types (communication & observation).
Incorrectly regarded as goofs: WALL·E's cockroach, Hal, sleeps in a "Kremie" (parody of the Hostess Twinkie). Twinkies grow stale and their cream filling evaporates after a few decades, yet Hal's interaction with it betrays it to be the same as a new Twinkie. This is most likely a joke implying that only cockroaches and Twinkies can survive the apocalypse.
Continuity: After Eve pops the bubble-wrap, she drops it to the floor, yet when the camera pulls back for WALL-E to dance, the wrap is gone.
Continuity: When WALL-E is climbing the ladder on the space ship, he climbs nearly to the top. Then he is knocked down from the force of the take-off. Then in the next shot, he is back at the top.
Factual errors: When they first show the axiom in space, it is in the midst of a nebula (similar to the eagle nebula). In reality, the nebula is giant; the size of a star (as a nebula is a cloud of dust and gases where stars are born). The Axiom is shown to be about the size of the nebula, which just isn't possible.
Incorrectly regarded as goofs: EVE probes are Extraterrestrial Vegetation Evaluators, but as far as we can tell they are only ever sent to Earth. However, while the vegetation isn't extraterrestrial, EVE certainly is. She is called "Extraterrestrial" because she is not from Earth's origin but comes from "somewhere else other than Earth" (the Axiom).
Incorrectly regarded as goofs: Towards the end of the film, oxygen masks suddenly comes down over all the humans' heads. Once the Axiom rotates and the people start to slide, the masks are gone. However, you can see the masks retracting back into the hover chairs as the ship starts it's tilting and the people slide out of them.
Continuity: In the scene where John and Mary catch the group of children, his hair is brown. In all of his other scenes it's blond.
Factual errors: When EVE breaks the sound barrier we immediately hear a sonic boom. Sonic booms are not heard until after the supersonic object has passed the observer.
Continuity: In the fight between the captain and Auto, the tiny steward is kicked through the window and is shown to crash at the edge of the Lido Deck, right next to the diving board. Shortly after that, when the captain presses the blue button, we see the Lido Deck as it's closing, but the remains of the robot are not there. In the shot immediately after that, which is shot from straight above, we can vaguely see the remains again.
Continuity: When WALL-E first meets M-O in the docking station, he leaves traces on the floor, which M-O tries to clean up. Then, when he hides from GO-4, he leaves no traces. Afterwards, when he runs after the cart, his traces are there again, so that M-O detects and follows them. Throughout the movie, WALL-E's traces only seem to appear in the scenes where M-O has to remove them.
Incorrectly regarded as goofs: When WALL-E first finds the plant he puts it in an old boot in his cooler, he never takes it out, instead it's still in there after he goes chasing after the red dot that signifies EVE's approaching ship. Later on in the film he takes the boot from a shelf in his truck to show it to EVE. Although the interval between the two scenes is relatively short, the intervening montage shows that at least one full day passes (EVE shuts down for the night). It is possible that Wall-E went back to his truck during the night and put the plant away.