WALL-E in particular brings out the pointless musings in us--maybe because Cars makes no sense in its initial concept (cars are the only living things on Earth? And they're...living?), so you kind of forgive the rest of its oddities as minor points in comparison. But WALL-E seems like honest-to-gosh science fiction, so you try to take it seriously; but as such, it has big silly plot holes. Examples:
If humans have managed to keep themselves alive and well on a spaceship for 700 years, including somehow creating food out of who knows what, surely they have the technology to go back to Earth and clean it up?
What is the Axiom doing out there in space, anyway? They appear to be just floating around aimlessly. Aren't they at least conducting some astronomical research? Looking for another habitable planet? It would seem not, which is really odd.
Of all the robots, why did they give the vegetation probe (EVE) the most lethal firepower? Wouldn't the power-hungry robots on the Axiom find a way to program in some similar firepower for themselves?
If said power-hungry robots (Auto and his cronies) didn't want the captain ever to return to Earth, why did they let him see the plant and the "time to return to Earth" message in the first place? Why didn't they steal the plant off EVE the second she arrived, and incinerate it, and never tell him?
By the way, the first plant that grows again on a barren Earth, what's that really going to be? Kudzu? Dandelion? Knotweed? I suppose it's still potentially edible, but quite unlikely to be the tidy little bean sprout they illustrate.
Also there are a couple of common sci-fi errors. For example, there shouldn't be any sounds in space (like the fire extinguisher's whoosh when WALL-E is using it to jet around). And the Axiom's gravity field would surely orient gravity toward the floor of the ship, no matter which way the ship was pointing, so spinning the steering wheel shouldn't make all the passengers go sliding to one end of the room as if they were on a boat in the ocean.
But, honestly, despite all those points, I think it's a delightful, clever movie. We still grin and giggle at certain lines and scenes. (The first time through, I couldn't stop laughing at WALL-E getting attacked by shopping carts.) The animation and artwork is astonishingly cool, the sound effects fun and creative. (I heard in a radio interview that for MO, the frenetic clean-up robot, they recorded the buzz of an electric razor.) I sympathize fully with EVE's fiery temper, as it's quite a lot like mine. (As my family acknowledges. Good thing no one equipped me with a laser arm.)
And I may never want to eat a Twinkie again after watching that cockroach burrow into it twenty or thirty times now. So that's probably just as well, as far as my health is concerned.