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: 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 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: How is it that the main character was able to follow her father's dead body to the coroner's office to see him put into a specific casket? She was a nine year old girl...no one noticed a little girl hanging around a morgue?
Suggested correction: Maybe the morgue workers didn't have the heart to eject a lone orphan from seeing her Dad for the last time?
Plot hole: About half way through the movie, the basketball coach is in his office and you can see a dry-erase board behind him, and a couple of dates such as 3-15-99... however earlier in the movie when they are announcing the basketball game they say that it is the 2000 season. They obviously changed the voice over to 2000 after the release date was changed, however the dates on the board are still referring to the scheduled '99 release.
Plot hole: When the police search the white car and the barn they fail to find the compartment in the car behind the boot in which the decoding equipment was hidden. This is completely improbable. It was a standard car, the compartment was not a secret add on, and the police were supposed to undertake a thorough search of everything.
Plot hole: Why can't people see the zombies until they are two feet away? Even in the daylight!!
Plot hole: In the middle of the film, after the custody hearing, Frank shows up at an event. Danny pretends that Frank dropped his wallet in order to have a brief conversation with his dad. Later, Rick confronts him about what they talked about. What does Rick expect? It's not like Danny will never be allowed to visit his father again. They are going to talk at some point. For Vince to expect that he will never talk to his father again is unrealistic.
Plot hole: When Margaret has to collect the $50,000, she goes around to various banks trying to get a loan on their house, which she can't get because her husband, co-owner of the house, isn't around. Why couldn't she just have taken the papers, said she was going to take them home to her husband, forged his signature, and brought them back? You can't exactly say she has either moral problems or isn't devious enough, since we've already seen her stuff a body into a dinghy, toss it into the lake, and come back to her house looking fairly normal.
Plot hole: Why did the killer cut off the hot water? Did he think that Dorothy would come down and turn it back on herself with all those staff members in the house?
Plot hole: When they are investigating the small box that was pulled out of the trunk of the car, the one with the doll, shouldn't they be wearing more protection? They are only wearing protection for their legs.
Plot hole: When Grace Stewart sends Ann out of the music room for "lying," the hall is visible as she opens the door - with lots of light from windows bursting in. I know it turns out not to matter, but the child would have screamed.
Plot hole: Jack is observing Maldic, one of the hijackers, while he is checking in at a London hotel. Maldic receives a message, and after he has read it he throws it into a garbage bin. However, at this particular moment Jack is looking discreetly into the opposite direction and should have no reason to look for the message in the garbage bin later. (00:48:00)
Plot hole: The kids in Soneji's class use an encrypted GIF algorithm to pass notes to each other and that "drives the teachers crazy", since they are unable to catch cheaters that way. But how do they do that? Easy, they have a message system in place installed on their workstations, that warns them with a big pop-up that they've got "A new message"! It would be easy to sanction and prevent the cheating by simply removing the chat application, no matter if they use it to chat directly or pass Michael Jordan photos as shown in the movie, which they have no business doing during an assignment anyway.
Suggested correction: The Spinosaurus used its full body force to smash the fence. The gate, being a smaller target, was too small for the Spinosaurus to use its full body force.