(at around 10 mins) When Leo enters the delta pod he puts on his helmet and it loosely touches the collar of his spacesuit. In the next shots it fits perfectly in the collar.
The scratch on Leo's neck swaps sides and disappears randomly.
(at around 24 mins) When Thade's niece buys their human pet, the bolt on the cage is left out. In the next shot, it's bolted shut again.
(at around 1h 6 mins) As Leo begins to enter the water with Ari on his back, she puts her hands over his face. In the next shot from further across the water, they are by his side. The hands return over his face once they are in the water.
(at around 8 mins) When the chimp is taking off from the ship you see Leo with his hands behind his back. In the next shot you see them at his side.
Chimpanzees, gorillas, and orangutans are apes, not monkeys. The script incorrectly uses the term monkey several times, but there are no monkeys in the film.
(at around 5 mins 20) Grace Alexander (Anne Ramsay) asks "Was the Homo sapien mean to you?" instead of "sapiens". The final "s" is distinctly missing (also in the subtitles) in the scientific way Lt. Col. Alexander talks about the "human" Davidson (Mark Wahlberg).
(at around 26 mins) When Leo is holding the branding iron close to Ari's face, the hot part of the iron is obviously painted orange to appear hot, and stays that color way too long.
(at around 1h 40 mins) After the chimp gets into his cage, we see an ape with his makeup incomplete.
(at around 45 mins) As Leo and co. escape the city through the tunnels, they break through some boards covering the tunnel exit. One of the boards has been clearly sawn through and is broken at that point.
When Thade forces Davidson's mouth open and looks in, a metal crown can clearly be seen. This should have been noticed by Thade.
When Leo first encounters the apes (as they are hunting the humans), Attar (one of the gorillas) hits him upside his head with the back of his hand. The blow sends Leo flying several feet upwards and backwards into the air. Any hit this powerful would have killed him instantly, most likely by breaking his neck or tearing his head off. Yet when he lands, Leo just picks himself up and carries on running. He doesn't even have a bruise or broken bones from the ordeal.
When Thade tells Attar and Ari to get him out, they claim they can't due to the hand scanner. But actually everything in the ship is new to them and they don't know how to operate it.
(at around 45 mins) When Leo and co. come out of the lost city there's a shot from some distance, back at the ship. Look to the far right and you will see a road with clear tire tracks on it.
(at around 1h 35 mins) During the final battle, studio lights are reflected on Thade's helmet.
How did humans from far and wide hear about "this human who defies the apes"? Leo was hardly noticed by anyone but the group he was with, and a few apes. The apes wouldn't publicize that a human was making fools of them, so how did word of his presence spread??
After the refugees cross the river, they set up camp and make fires. They are in the middle of the desert and there are no trees as far as the horizon. Where did they get the firewood?
It is not explained where the horses originated. They weren't on the Oberon.
We first see Captain Leo Davidson training a chimpanzee in astronautics. Its inconceivable that an officer with such responsibility would be unaware of the taxonomic and cladistic difference between apes (including chimpanzees and humans) and monkeys (the New World and Old World monkeys). Yet he twice refers to his student as a "monkey".
The monkey in the pod that is launched at the beginning is shown in a full spacesuit except he is not wearing any gloves.
After the battle when Leo traps Thade in the Oberon's command center, Thade tries to talk Ari and Attar into letting him out. However, neither would be able to let him out as the palm prints would be programmed into the security system and neither of their palm prints would be stored.