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: Check out the final routine at the end of the movie for the Clovers. Watching carefully, approximately 20 seconds into the routine you will see two girls on the left hand side running face to face into each other. If this had been a proper competition they would have lost because it was a major error in the routine.
Plot hole: In the Redstar mainframe, we are told that the floor of the vault will trigger the alarm if it receives more than 0.25 seconds of contact (apparently even with the security checks). What would be the point of the bosses going through all of those security measures if they would just set the alarm off anyway? Surely once the girls have faked the fingerprint and retina scans, they don't then need to flip across the floor! (00:33:55)
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 Fluffy saves Chloe she calls out 'thank you Fluffy'. Cruella never told her the dog's name so how did she know it?
Plot hole: Ginger can hold Mrs. Tweedy single winged. She can also tip up a feeder full of food. So now we have clarified that she is one ridiculously strong hen, how does she need help pushing up a deck chair? 3 other chickens were able to do it with ease earlier.
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: In the makeshift morgue when Simon and Matthew first fight the vampires, Solina is shot and pinned to the wall with a large silver nail and remains calm and unaffected. However, moments later Marcus is fighting with Simon and grabs one of same kind of nails but must drop it when it burns his hands. It makes no sense that Solina had no adverse reaction to the nails at all when Marcus reacted so violently. (00:42:00 - 00:57:50)
Plot hole: When Wolf and Tony find Virginia in the Huntsman's tree house, she tells them that he chained her up, so she can't go downstairs and open the door from the inside. However, after Wolf climbs her hair and enters through the window, the two of them walk down the stairs without any chains stopping her. They couldn't have cut her free with the magic ax because Tony was holding it, and he was downstairs by the door.
Plot hole: There's no visible evidence that Team Rocket has taken away Ash, Misty, and Brock's Poké Balls when the gang was in the cage, so why don't the Trainers call out their Pokémon (Brock's Onix would've helped out very much) and escape the cage?
Plot hole: Referring to that blackout night. How come the group can actually film how they put all their cameras and stuff into its hide?
Plot hole: When Alex and Clear are sitting and having coffee they are on a corner. He looks in the window to see the bus pass, and as he looks to see if it is there, it's not. As the camera pans across the street, there is some construction going on which is blocking that whole road from being used, but then Terry, Carter's girlfriend gets "waxed" by the bus - no way it could have got through all that construction.
Plot hole: In Jonathan's ballet at the workshop, Sergei proceeds very slowly through an array of twenty dancers before reaching the leading lady, whom he expects to be Maureen. But instead it is Eva, whom Maureen has asked to take her place. When Sergei sees Eva, he is extremely surprised. I guess that could make sense, if he's been focused on his own dancing. But the stage crew and several dancers in the wings start chattering confusedly, as if they've also just seen Eva for the first time in that same moment. However, Eva must have been standing there for several minutes, or at the very least had just walked through the crowd of surprised people, and Maureen must have been missing from her spot this whole time, so these people should be in mid-reaction. (01:26:50)
Plot hole: Despite being whipped and needing to go to the hospice afterwards to have her wounds seen to, when we see Madeleine later in the film she doesn't act as though she had whiplashes across her shoulders - she lies on her back that very night in bed, and gets up without a wince, she holds her shawl close when she is wandering around the asylum, she leans back against chairs, and in all the later scenes she is still wearing her tight bodice, despite the fact that such wounds would have been very painful for ages afterwards.
Plot hole: Near the end of the movie, Lance approaches Leon saying he's waited longer for this than anyone; however, he stated earlier in the film that the first encounter between Leon and his wife was in 1990, and another member of the V.S.A. said Leon and his wife were together in the Spring of '89, meaning he would have waited longer than anyone.