Minor Plot hole: The Axiom ship is said to have been operating for at least 700 years. It is also said that it could last that long because everything was recycled. This nonetheless creates a contradiction with the huge waste facilities on the ship that dump tons of waste every day. (operated by giant Wall-Es)

Plot contrivance: At the beginning of the movie, Wall-E finds a newly grown plant inside a perfectly sealed safe. It is however impossible for plants to grow without sunlight.