In the closing credits for Special Thanks, Bobcat Goldthwait's last name is misspelled as "Goldthwaite."
Every species of animals who goes through the High Evolutionary's "millions of years of evolution" process end up humanoids, which is a very anthropocentric cliché.
You don't freeze in vacuum. you boil. put a glass of water under a bell glass and watch it start boiling.
(at around 1h 12 mins) When the girl is running in loops for the High Evolutionary, her long hair does not fall down towards the floor when she is upside down. It stays in place behind her shoulders (defying gravity).
The two ships have a huge hole on their sides and yet no one is affected by the vacuum of space unless they "step outside".
(at around 1h 40 mins) The creatures on Counter Earth are mostly evolved from mammals, but one of them is clearly of avian origin; she has breasts, which only mammals have.
(at around 57 mins) Smart survivor Gamora gives away her location to a stranger despite obviously not recognizing their voice.
(at around 1h 30 mins) Not the best move to remove an electronic piece of equipment in water. It could then very easily malfunction.
The High Evolutionary needs Rocket's brains and yet sends a rookie who traumatizes him.
(at around 5 mins) These heroes should know never to put to bed an intoxicated person on their backs but always in the recovery position.
(at around 1h 45 mins) Rocket doesn't try and shoot down the flying robots coming at him.