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.
Unaddressed Issue: In this incredibly advanced future where robots take care of every single human need, why don’t they use liposuction to get rid of the fat? Wouldn’t it be effective to use that fat for other things in the ship since everything needs to be recycled in order for the ship to be sustainable forever? If every next generation gets fatter on the ship: there is less food for everyone else.