Plot hole: The "video history" of the crashed USAF ship makes it very clear that the planet is uninhabited when they "landed". I can understand how a race of apes develops - they had a bunch of them on board. I can understand how a race of humans develops - they are descendants of the original crew. What I don't understand is...where the heck did all the horses come from?
Plot hole: Anubis Warriors can only be killed by being beheaded. But during the final battle, you see several are killed by simply being stabbed.
Plot hole: Where do the flyers come from that are in the bags that are carried out of the vault and into the van? Danny and Linus couldn't have taken them down there and there is no room with the Chinese man. They are carried out to the van before the SWAT team appears, which means they'd have to have been in the vault to start with? In the commentary by Steven Soderbergh he acknowledges that there's no explanation. (01:35:05)
Plot hole: Spoiler: At the end of the film we learn that the girl is the wild animal, having been saved by the same doctor. Yet at the restaurant she is wearing a bare back dress and does not have the giant X-like scar on her back, like he has or the model has, who the doctor marries at the end.
Plot hole: The spinosaurus manages to smash through a metal reinforced wall designed to stop dinosaurs getting past it without too much effort, yet it can't get through a wooden gate secured by some metal bars. It makes no sense.
Plot hole: How could the police miss finding Cybil in the trunk of Michael Zane's car when it was in an impound lot? They would have definitely searched the car if he was found in violation of a federal offence (for carrying the weapons). Even if they didn't do a search, they would certainly have heard the sounds that Cybil would have made from being locked in the trunk.
Plot hole: When Carlos (Bill Maher) is explaining to Michael what was a valid roll he says that the redhead rubbed the dice on her chest for good luck and threw them. However she immediately threw the dice when Michael handed them to her. She only rubbed them on her chest and gave them back to Michael on a prior roll.
Plot hole: When the Grundel explodes near the end, Rowan looks out the window to see Uber Jason floating towards the rescue shuttle, only to be grabbed by Brodski who happens to fly sideways at a high rate of speed. Now provided it's feasible that Uber Jason can survive an immense explosion, how Brodski not only survived the explosion but managed to wind up away from the spaceship and far enough off to the right so as to catch Jason in mid-space is beyond me. (01:22:15)
Plot hole: Stuart establishes that there is only one of you and that when you travel through time you can repeat things, but it will be you and not your double that does it. But, at the end, when the Duke is going up the stairs and the uncle says "Where have you been...", the Duke is wearing the same clothes as the first time. Yet we see that he goes directly from the time portal to his house in the ballroom raiment of the later scene. Where did the old clothes come from?
Plot hole: On the doors inside the white dome, and on the elevator door, it is marked "Vapor Lock." This is impossible due to the mine shaft opening. It can't be vapor locked when there's an opening. (00:35:00)
Plot hole: When the security guards enter the cage housing the blown safe there are no traces of the water used to break the safe - not even on the (dry) floor. This happens only minutes after the explosion sent the safe door and gallons of water across the cage.
Plot hole: When Martin decides to antagonize David by eating spinach, he eats it from his plate. When they both eat the spinach frantically, they each eat out of a large bowl. Where did the second large bowl come from, and why would there even be a second one if they only need enough for three people? (00:34:55)