Revealing mistakes: The tow cable for the raft costume is visible.
Boom mic visible: While Woody is describing the artifacts from the 1970s.
Revealing mistakes: When Woody is trying to escape with the flying device (the one that mounts in the back) the tow cables are visible in one shot
Continuity: Luna's shoes change from high heels to flats when she crosses the lake on Milo's back (in the "raft" costume).
Continuity: When Woody is stuck in a tree, he is wearing blue jeans, but both before and after that, his pants are black.
Continuity: When Miles is first awoken from the cryogenic freezing process he has tin foil under his suit. During the process of sitting up, the foil mysteriously disappears from around his neck/chest area.
Factual errors: The rubber tires on the Volkswagen could not have survived 200 years in the open air.
Factual errors: The Volkswagen could not possibly start after 200 years in a cave. Gasoline typically has a 30 day shelf life. After 30 days the aromatic parts of the gasoline noticeably start to evaporate, and it begins a chemical breakdown process into gum, resin and varnish which cause misfires and poor starts, poor performance, and could cause engine damage. Degraded fuel in a running engine also leaves deposits in the carburetor plugging essential passages and can also leave deposits on the intake valve stem causing it to hang up and not close properly or even not to close at all.
Factual errors: The Volkswagen's battery would have long since died.
Revealing mistakes: When Luna swings across a creek the action is performed by a male stunt double in a wig and the character's outfit.
Plot holes: The whole point of reviving Miles is to have someone without any record in order to infiltrate the Aries Project, but Luna is able to do so just as easily despite the fact that she is a known fugitive.