Plot hole: Why on earth would the military be interested in a soldier (sailor, aviator, whatever) who has to go into combat naked and unarmed, and who is detectable by an enemy equipped with a pair of cheap, mass-produced goggles? How would you treat them if they were injured? They would be utterly useless in any form of military operation, even espionage.
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: 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: It has already been mentioned that a certain shot reveals that Sidney isn't wearing the bullet-proof vest when she should be. Further to this, most of the shots in the climax sequence make it impossible for her to be wearing one, as you can see the contours of her chest throughout. A bullet-proof vest would flatten the appearance of this.
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: 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: 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: 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: 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.
Plot hole: After Jade sees Jaspers transform, she flees and calls the cop Margolies on his cell from a pay phone. It's pretty unlikely that in her panicked state of mind she'd remember his number by heart, especially since he only gave it to her that same day.
Plot hole: The scene where the sisters are talking about killing the popular girl in class during P.E. during a game of Lacrosse, Bridgette is pushed into the body of a disemboweled dog. Everyone then starts to freak out seeing the dead animal. How could anyone, the students, teachers, grounds-keeper, not see that corpse until Bridgette was knocked into it?
Suggested correction: Presumably the military are interested because Sebastian's research could lead to advanced forms of invisibility technology, such as the ability to turn materials and weapons invisible for use in combat.
You cannot second guess the film like that. Sebastian is making no effort to make non-living items invisible and throughout the film we see that is not possible (why else would Sebastian have to walk about naked?). His research is on animals (and later humans) not "materials and weapons" and is based on their physiology, anatomy and metabolism. How would you inject a rifle or a tank with a serum? They don't have a bloodstream. The military wouldn't see any value at all in this research - maybe they would be interested in invisibility, but not if it was restricted to living creatures as we see here.
You know how easy it would be for an invisible person to infiltrate an enemy's compound undetected and take out powerful leaders or dictators? Especially if no-one knew the technology existed.
Easy? Impossible. First, they would be naked and unarmed. Too bad if you are trying to knock off Vladimir Putin - a taekwondo black belt - with your bare hands during a Moscow winter! Being invisible doesn't mean you can avoid making a sound or triggering a pressure plate or an infrared detector and so on and so on. Final answer - a naked, unarmed combatant would be about as useful as a chocolate teapot in any form of operation, covert or otherwise.