Plot hole: The opaque red lined map that Otomo retrieves from his first fight is ridiculous. Why would people who know where the hidden base is be carrying around a map on them (which shows a route so basic that they'd have to be brain-dead not to be able to remember it anyway) just so that conveniently one of their enemies can get it?
Plot hole: This happens after Gabe has killed the guy in the cavern and is reaching for the radio. We hear Frank trying to reach them, so they must be on the same frequency. Then, Hal finds out that a bomb has been planted, grabs a radio from the bad guys and starts yelling for Gabe to get out of the cavern because of the bomb. Why didn't Frank hear any of this on his headset?
Plot hole: It would seem to go against Secret Service procedure (as well as National Security) for an agent like Frank to give such an openly candid interview to a magazine such as Esquire.
Plot hole: In Cayman, Abby drugs Avery's drink at dinner. It takes effect as they return to the bungalow, and Avery passes out on the foot of the bed, fully clothed. In the next shot, Abby is in the kitchen, carrying the Mafia files. The bedroom is seen in the background, only now Avery is under the covers and without a shirt. After being knocked out by a "Mickey Finn," he wouldn't wake up, undress, and get into bed. Nor would Abby be able to do this - he is too heavy and bulky for her to move and undress alone, plus she would not have enough time to do that and also transport the many files, get them copied, and return them to the bungalow before Avery awoke. Avery would also be suspicious, knowing he was ill and had passed out atop the bed, but awoke undressed under the covers.
Plot hole: There is a guard stationed in the time lock vault without oxygen. Also, if the vault was supposed to be that secure, why were there simple bars protecting the back entrance?
Plot hole: Darby goes to great pains to get out of the country, to where no one will know where she is but Grantham. But upon reaching her "secret" destination, a van pulls up to the plane and a man gets out and hands them an envelope with a copy of the front page of the Washington Hearld with their breaking story and both their names as by-lines. That couldn't happen unless other people besides Grantham and the pilots knew her destination.
Plot hole: Just after Rita rescues Jeff, Diane's grave is seen close to where Jeff was buried alive. Even though Diane's been dead for several years, her make-shift grave site looks like it was freshly dug. There are no fallen leaves or other debris on top, no new vegetation (moss, grass, weeds, etc.) of any type growing on it, nor has the mound of dirt settled, shifted, or been affected by the weather.
Plot hole: Foster served in the military and even received a Purple Heart as indicated by the plaque in his mother's home. Yet he needs a kid to explain to him how to handle an M72 rocket launcher. A weapon introduced in the 60s and thus well within his time at the military.
Suggested correction: Not everyone in the military knows how to use this particular type of weapon. In fact, probably most don't.
Plot hole: In the scene in the hotel, David sees the victim's head on the floor after the killer left. Later when David is in a hospital bed he is watching TV and the reporter claims that all the heads were in Judd's car. The killer would have had to have gone back into the hotel room to get the head of that victim after David saw it. She would have put it in her bag right away if she was saving them all. The bag was even left behind. (01:12:30 - 01:25:00)
Plot hole: There's a number of strange things about Butch's and Terry's escape: When the grid falls down the very loud noise passes unnoticed. After they climb down the tied bedsheets Butch pulls once and it comes down, although no-one tied it loose. And finally, their escape route ended within the prison walls, and they needed to kidnap the clerk, who had come back into the prison to get some papers, for the escape in his car, something which wasn't planable at all. (00:05:40)