Plot hole: The group poison a dozen or so people and dispose of their bodies by burying them in their own garden. Some of their victims are notable celebrities - television presenters, authors, leaders of large and vocal pressure groups. Certainly some of them are nobodies, but nonetheless they are going to tell friends where they are going for dinner! Not one of these people told their assistants or their secretaries or a friend or a relative - a spouse? - where they were going and what they were doing on the night they were murdered? Not one of them? Not one single trace was left for the police to follow? Absolutely impossible.
Plot hole: Stephen dies after he was "taken off machines", at least so his wife tells the kids. But when he was shown in the hospital he was attached to no life-supporting machines except an oxygen tube in his nose. (01:33:25)
Plot hole: Alain joins the Legion, goes through extensive training and eventually gets his photograph taken. That's how Galgani recognises him and sends two men to kill him. They arrive with a platoon at the fort just after Alain, Mackintosh and Luther. The photograph would have taken a while to get back to France and then the two men would have to go through the same training. So how do they both end up in the same fortress after they joined the legion long after Alain?
Plot hole: When Eldon checks out the address Van Meter gave him he finds where Orchard and Sidwell are living. All well and good, except: A) The utilities bill is in the names of Orchard and Sidwell, who are known wanted felons in L.A. and B) even more implausibly, the bill is in BOTH their names.
Plot hole: When the two Legionnaires open the gate of the Hadrian's Wall, they lean forward with their shoulders against the doors as if to push, but they are really pulling. (00:33:10)
Plot hole: When the policeman asks Kirsty at the beginning who came when she solved the box she says the Cenobites; she had no way of knowing what they were called. Frank only told Julia; Kirsty didn't hear it anywhere and the Cenobites themselves didn't tell her either.
Plot hole: When Dan is chasing after Carter to catch him and Alex together at the restaurant, there's very little chance he could have had any idea where Carter was going. He couldn't have told the cab driver to "follow that taxi" because in the time between Carter getting in a cab and Dan getting in a cab about 5 taxis drive past, so how he happens to end up at the same place is a miracle.
Plot hole: Krell doorways and equipment suggest they are short, wide and 2-3 times larger than a human. Yet the shuttle pod the Commander, Doctor and Morbius ride in is designed for human size beings.
Plot hole: The timing in the film is way off. Given the hours when JM Inc is open, most of the people there would only get to be Malkovich while he was asleep (yes, films have late-night shootings, but not every night); and Craig and Maxine stay up the whole time, then mess with Malkovich afterwards, then get in for work the following morning without showing any sign of fatigue even though there are less than 2 hours left for sleep.
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: Klaatu is shot and his body is lying in a prison cell. Gort leaves the flying saucer and walks all the way to the heavily guarded police station in downtown Washington DC. Gort is 8 feet tall and is a robot plus he uses his noisy death ray to create a hole in the police station to retrieve Klaatu's body and nobody noticed him? On top of that, he walks all the way back to the saucer unseen with a dead body. (01:22:36)
Plot hole: When Ritchie appears at a pizza party sponsored by a local radio station, his manager Bob Keane is handing out copies of Ritchie's first album. In reality, the album had not been released until April 1959, two months after Ritchie's death. As the actual LP includes his biggest hit "Donna", Ritchie had not yet recorded (or even composed) the song in this part of the movie until a few scenes later.
Plot hole: When the "black diamond" is being turned into its dangerous form, the arms dealers get very excited. Yet all they actually see is a very pretty laser show. There is nothing to show that the object really has any destructive power. Arms dealers make their fortunes by being cautious and smart. They shouldn't be so quick to accept the claims of the bad guy and bid money on possibly useless stones. (01:18:20)
Plot hole: At the end of the movie where David and his friends are attempting to break into Steve's house, David has the door code and attempts to gain access once by using it. Steve then tells his wife and the kids to go hide upstairs and turn off all the lights so nobody will know where they are. Then Steve and his wife go to another part of the house, away from the front door. Then, we hear David and his friends using axes and a big log to try and break down the door, "before* Steve secures the door with household appliances later on. Why wouldn't David have just kept trying the code?
Suggested correction: The reason David can not keep trying the code, is because the door has a lock on the top, and one at the bottom (middle regular lock). That middle lock is able to respond to the key/pass-code system, but the top one is not. In order to get in the house, David would have to be able to enter the pin (which, yes he knows) but with the top lock still locked from the inside he can not get in. I am assuming there is a key slot on the outside where he would need a key, and also I'm sure the family doesn't bother locking the top half of the door as no one else knows the pin (so they thought). And I'm guessing that they never locked it during the day either, and only at night.
Plot hole: At the beginning of the film Lustig suddenly emerges from the water right in front of Finn. It's not possible that he could have been hiding in the shallow water without Finn noticing him. (00:03:40)
Plot hole: The only reason Kate is brought onto Matt's team is to give the CIA legal authority to operate on US soil. Given that he already has DEA agents and US Marshals on the team, all of whom seem to be fully aware of what he is doing and have no problem with it, this doesn't make a great deal of sense. Her idealism makes her a poor choice for the sort of operations the team is doing, and there are already domestic US agents available.
Plot hole: During the Congressional hearing, it is suggested that the alien signal could have been faked from a satellite - as Ellie only has her own experience to go on, it leaves her believing what happened, but still with an element of doubt. However, as a professional astronomer, Ellie would have immediately dismissed this since a simple parallax (triangulation) would have confirmed that source was at the distance of Vega - a distance far too great for any rocket to reach. (This is mentioned in the book). In fact, this is mentioned early in the film, when the employees in New Mexico calculate the source of the signal while it is transmitting prime numbers.