
Plot hole: At the end of the film Mardukas reveals that he has been wearing a body belt packed with cash - "in the neighbourhood of three hundred thousand dollars" - ever since Jack detained him in New York. Are we to assume that Jack Walsh, an experienced, hard-bitten ex-police officer, now a bounty hunter who routinely chases down violent and armed bail absconders who would kill him without a second thought, didn't even perform a perfunctory search of Mardukas when he detained him? This man used to work for the Mafia! What if he was carrying a weapon? A body belt with three hundred one thousand dollar bills in it would be uncovered by even the most casual pat down.
Suggested correction: He was using $1000 bills. That's 300 bills in the belt which spread evenly absolutely could have been missed near his waist as part of his clothing.
Rubbish. I specified $1,000 bills as that would be the smallest package he could have secreted about his person, and it would still be instantly detectable. If he used $100 bills the package would be ten times larger, and he would have to carry a rucksack under his shirt.

Plot hole: Andy is suspected of having killed Eddie Caputo, because he was at the scene when Eddie's house blew up and Eddie was killed. But there are glaring things that go unquestioned: None of the cops seem to think it's strange that a six-year-old kid would travel by himself so far to some random house in order to blow it up. The South Side neighborhood where Eddie lives is halfway across the city from Andy's apartment. How did Andy know where Eddie lived? How do the cops think he even knew Eddie at all? None of them address this most puzzling problem.
Suggested correction: The police believe Andy to be insane (hence why he is sent to a mental institution instead of juvenile hall), and thus do not believe his choice of victims to be in any way rational.
Also, as unlikely as it is that a six-year-old child could (or would) travel halfway across the city to murder a random person, the possibility that a child's doll came to life and carried out the act was considered far too outlandish at that point in the plot.
Suggested correction: We don't see the entire investigation. We just see the cops holding Andy then taking him to a psychiatric clinic. Chances are they were asking those questions and we just didn't see it because it's not important to the plot. Regardless, the cops have every reason to believe Andy either knows about or was partly responsible for the murders considering he keeps showing up at murder scenes. There's only so many conclusions you can draw, even if they don't make sense.

Plot hole: When Kalgan is torturing Lea, he says that he wants her father's countermeasures in case of emergency. But when she is rescued and finds out MacPhearson is a traitor who is working for Kalgan, Captain Devers is worried because MacPhearson knows all of the ship's countermeasures. If MacPhearson knows the countermeasures, then Kalgon does too, so there is no reason to bring it up while he is torturing Lea.

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: After they shoot the glass and McClane escapes, the terrorists all just leave. There are limited ways out of the room, there must be a blood trail over the glass, he's moving slowly...and they let him go.

Plot hole: When Gary Busey infiltrates the Mexican terrorists' compounds, he first throws a stick to distract some guards and kills them. A few minutes later a terrorist officer reports to his boss that Gary Busey has killed three of his best men. Are we to believe that the three best terrorists were tricked by a stick thrown into some bushes, and then easily killed by an unarmed assailant (they had submachine guns)?

Plot hole: Les comes home and tells his parents he passed his test. A scene later, his mom is going through the laundry and takes the test out of his jeans pocket. How did it get there when Les is still wearing the same outfit he wore to the DMV?

Plot hole: While Harrison Ford is taking a shower shortly after arriving at the hotel, the 'bad guys' kidnap his wife from the hotel room. How did they know she was the one who had picked up the wrong suitcase (which contains what they are after) at the airport? They could only have assumed that. And the suitcase they were after was in the room so why didn't they just take it?
Suggested correction: Ford himself explains how they know she picked up the wrong suitcase. Emmanuelle Seigneur grabs Ford's wife's suitcase by mistake, and puts it in the locker to be collected by the bad guys. The bad guys then go to the locker and get the suitcase - only to discover it's the wrong one. Ford specifically mentions her name and address tag is on her bag, so they see that, and immediately know who to look for.
But, why did they have to kidnap her? They could just take the suitcase and leave her alone. They came all the way to her room but not looking for the suitcase?
Good point, but that still doesn't explain why they simply didn't take the case from the hotel room instead of kidnapping Mrs Walker and holding her ransom for it. Suggested answer - they wouldn't have been able to make a movie out of it.

Plot hole: It is explained that due to the severe beating/stabbing Cordell received in prison, he has no "higher brain function." How does this make him impervious to gunshots?