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 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: Towards the end of the movie when Michael Douglas makes his speech at the White House, he is able to quietly walk out of the gates with no reporters anywhere trying to chase him down. Totally unrealistic (especially considering what had just happened). (00:03:03 - 02:13:40)
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: Junuh gets the lowest score on the 17th hole in the final round, which puts all the players at 'even'. It should therefore have been his honour 18th tee. He actually tees off last, which would indicate that Jones and Hagan had bettered (or at least matched) his score on the 17th.
Plot hole: The attack on Israel scene leaves one important question: How would it have been possible for the bad guys (the Russians, or Arabs, or whoever) to stage such a massive surprise attack without being discovered ahead of time? Anyone who is knowledgeable in modern warfare would know that an operation of that scope would require a considerable amount of logistical preparation that could not possibly go unnoticed, especially considering the capabilities of modern spy satellites.
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: In the scene where Willie takes Skip to the army recruiter, the recruiter classifies Skip as 4-F because one of his testicles hasn't dropped. But seconds later when Skip stands on his rear feet, it is apparent that Willie, well let's just say that a pair beats an ace high.
Plot hole: In the several scenes at the hotel when Carlo and Bonehead confront Jack there are a total of 9 shots fired in the hallway and another 30 ultimately fired in the room as well as a chair thrown through a window. Although we were able to hear a baby crying in another room when Jack initially climbed the stairs no one seems to hear the monumental confrontation for a very long time or look outside their rooms to see Bonehead lying dead in the hallway. Carlo has an enormous amount of time to patiently question Jack and make phone calls. When sirens do arise after a long while, the very first responders are the Feds screeching up in their big red Caprice followed by some police. Somehow the US Treasury Department is able to get to the scene faster than the police.
Plot hole: After the marines fire into the crowd and things die down, Jackson tells his men to stay down because of possible snipers. Yet he is standing upright the whole time. Not the best tactical move. One sniper and the mission loses its commanding officer.
Plot hole: When Rudy removes the leg of the bed to escape from the motel room, he finds Charlize Theron and Gary Sinise in the pool. He walks away saying something to the effect of "I am out of here." As he trys to escape, he keeps running into the other members of the gang and has to rush back and pretend he is still handcuffed to the bed when they check on him. If he is already free of the bed, why doesn't he leave after the gang goes to sleep for the night?
Plot hole: Towards the end we see Jones ring Derrick to warn him that Travis has a gun - why would she do this if it's all planned? why risk him picking the phone up? he would have escaped before Travis had time to stop him and get him back inside to finish the set up. This scene is purely for the audience to be more taken in and shocked at the actually twist. (01:17:00)
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?
Plot hole: After witnessing two friends getting killed by massive shark bites (as well as Richard's shark encounter) they all choose to swim away from the island together; even though Sal and Richard used a boat to get the mainland carrying multiples bags of supplies. The newcomers also arrived with multiple kayaks which Richard was aware of before seeing them all get shot.
Plot hole: In the movie the German sub is in the middle of the Atlantic about 1500 miles from the American coast the American submarine is an S-Class boat which had a top speed on the surface of 12 Knots even less underwater and it spent part of the trip submerged. This means that it would have taken them at least 5 or 6 days to reach the German Sub. This is 1942 There would have been dozens of other German subs a lot closer who could have come to their rescue.
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.