Plot hole: There must be a lot of dumb scientists in Sebastian's lab. While defibrillating the invisible gorilla, (s)he becomes completely visible for a moment. However, not once do the scientists consider that applying a mild electrical shock to the system renders the invisible animal visible again - that electricity may be the key to the whole invisibility problem. They don't even comment upon the fact that the gorilla does become visible.
Plot hole: Peter goes into Carl's mind to save Catherine. When he's in there he sees the tank with the water nymph. On the tank are strange symbols which provide the FBI with the clue needed to find the latest victim. Makes sense so far. But, go back to the scene just after the FBI have captured the comatose killer and are looking in his basement. The FBI are looking at the contraption that the killer uses to suspend himself over the victim. On the contraption is the same symbol seen later on the water nymph's tank. Why didn't the FBI follow up the symbol then?
Plot hole: The facilities at Ft. Hood have working electricity to power the simulators, projectors, etc. even though it's been 1000 years, with no logical reason for the Psychlos to have kept the facility maintained, and the fact that the Psychlos should by rights have leveled the place when they invaded 1000 years before. Even automatic backup generators would have no fuel after 1000 years dormancy except for a nuclear system, which would still have required regular maintenance over a 1000 year interval to maintain automatic functionality.
Plot hole: When Tim Robbins is floating away in space his wife could have easily saved him. She could go out a little further, use the grappler to catch her husband, then use the fuel she has remaining to halt their acceleration towards the planet and return them partway to the necessary orbital altitude/velocity to rendezvous with the resupply module. Then, Gary Sinise could come out partway to them using his thrusters, Connie could shoot the grappler out to him, and he could reel both Connie and Tim Robbins back in to the resupply module.
Plot hole: After Nanahara and Noriko run away from Akamatsu at the school, Niida shows up from behind some bushes opposite the school and inadvertently kills Akamatsu with his crossbow. But Niida is Boy 16, which means he should still be in the school building (he's supposed to come out after Noriko, who's Girl 15). There's no way he has any time to get into those bushes.
Plot hole: When Captain Towers gives his XO an injection to allow him to die in peace, he, properly, swabs the site with alcohol, and slips the needle into the vein. However, immediately below the injection site, is a hep-lock.a port installed into a vein to allow injectables to be administered. I cannot imagine that a senior Naval officer would be so ignorant of the port's function.
Plot hole: How did Carolyn Fry get out of the cave in the canyon to confront Riddick at the Skiff? Riddick strained to roll the rock into the cave entrance, and he was a big, strong man from a position of good leverage. How did Carolyn and the other two push the rock out of the way so that Carolyn could get out? And, then, how did Carolyn mange to push the rock back into place? It was still there when she and Riddick came back from the Skiff to bring back the other two.