Plot hole: When Charlie sets out to hijack the money train, he jumps off the platform onto the tracks as it arrives, in plain sight of the driver and other passengers at the station, and only puts his mask on once he's in position on the tracks. The train conveniently stops right over top of Charlie, allowing him to enter through the conveniently-placed grate on the train's floor. (01:17:15)
Plot hole: Now why the heck is one of the stealth fighters anywhere near the train? Stealth fighters use advanced targeting and do not need to be anywhere near their target, yet in the movie the one fighter is so close to the train when it gets blown up that it looks like it's on a collision course.
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: When SWAT enters Peters wife's room, the officer reaches for her neck and almost as soon as he touches her, he states "no pulse". This guy's EMT skills are phenomenal! Carotid pulse with a glove on in less than 2 seconds. This guy is good.
Plot hole: In the scene where William takes Murron for their initial ride, he shows up in pouring rain, yet all further shots show the two of them totally dry. The tone of her mother's voice when they get back suggests they did not spend the night together, and the whole sequence appeared in a couple hours. They could not have gone from soaking-wet to bone-dry that fast.
Plot hole: In the scene after the bank job where Charlene waves Chris off alerting him of the setup, Chris drives away and is stopped by the cops to verify who he is. He has a fake ID and they let him go. The police CLEARLY know who Chris is and what he looks likes for most of the movie but somehow, those cops don't have anything with Chris' name and face on it?
Plot hole: When Bo-Tat is purchased the Village Elder insists that Lihn go with Bo-Tat, it is CLEARLY established at this time that A) Lihn is an orphan and B) his parents were both killed in the war. For two-thirds of the movie Capt. Doyle repeatedly comments that Lihn can't be trusted because we don't know who (NVA or USA) killed his parents. There is no possible way that Spc.5 Farley wouldn't know this. However, halfway through the movie (on the river boat) he asks Lihn where his parents are and how they died. He couldn't possibly be ignorant of this, since he took part in at least two of the prior conversations.
Plot hole: Jose is the only one carrying the bag of money, then he gets killed, in the next scene Anthony and the others have the bag on the table though none of them were carrying one besides Jose.
Suggested correction: Kirby and Klingon were both running with bags of money.
Plot hole: The premise is that the back-story is a fabrication, including the five being placed together in the police line-up and in custody in order to get them to work together. But in the flashback of Keaton in the restaurant, it is Dave Kujan who takes Keaton in. It is inconceivable that Kujan would be complicit in the staging of the line-up (and doesn't fit with the plot). And if Verbal is inventing it, then Kujan is going to know it didn't happen. It doesn't make sense and undermines the plot.
Plot hole: After leaving the hospital, Racine ducks into a pachinko parlor. In there, he gets a young girl to help him find a telephone and a taxi. The problem is, she is about 10 years old, and you have to be 18 to even enter a pachinko hall. The attendants we can see in charge would have evicted her within minutes.
Plot hole: When Injun Joe is about to kill Huck, Tom takes notice of the chest full of gold coins and then empties the chest out (offscreen) because it was too heavy for him to lift, and then tricks Injun Joe into trying to retrieve the empty chest, resulting in Injun Joe falling to his death. The amount of time that passes between Tom glancing at the chest and then tricking Injun Joe before he can kill Huck is roughly 5 seconds. There's no way Tom could have emptied out of the chest in that little amount of time if the chest was too heavy for him to lift in the first place, especially without making a sound.