Plot hole: The idea that Ben Gates had to run away despite the President's being okay with the kidnapping does not make sense. The President could simply pardon him if necessary. However, when he ran away, he would likely be committing other crimes (fleeing and eluding police, reckless driving, etc.) that would not be federal crimes and so would not be pardonable.
Suggested correction: That's basically what he did at the end. Even though the President was OK with Ben "kidnapping" him, if Ben didn't find the lost city of gold he would have been arrested and charged for kidnapping the President (amongst other charges). However, because Ben was able to find the city the President gave him and his crew a full pardon and explained that it was a misunderstanding.
Plot hole: Tommy leads the mob after the 2nd escaped patient, thinking it's Michael, but Tommy should have known it wasn't Michael. He saw the patient on the TV at the bar at the beginning of the film.
Plot hole: Toward the end of the movie, it is revealed that Silvia spent the night in the secure room where the Matabo President was taken after the assassination attempt so that she could be alone with him and threaten to kill him. With the U.N. and Secret Service on alert for an assassination attempt, wouldn't they have swept the secure room right before the Matabo President arrived that day? In addition, Silvia would have had to use her access card to get in that area of the building, so there would be a record of her being in the building but not at her station. Wouldn't that raise some suspicion long before Tobin figures it out?
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: When the President of the United States attends a public gathering (such as the SuperBowl) the level of security is extremely high. So why wasn't Mason's delivery on the day of the game checked for explosive devices?
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: The fearless trio is in the watch tower when the hillbillies set fire to it. Realizing their fate if they stay, the three then jump out the window and onto nearby tree branches in order to escape the blaze. After escaping the towering inferno, it seems that the fire dies immediately. These three don't go far after jumping and are in the trees for some time. Shouldn't there be a great glow and lots of noise and smoke from the fire as the watch tower burns down? (00:53:45 - 00:56:00)
Plot hole: When the deputy arrives at the sheriff's house, Michael gets out and leaves the door open. The deputy comes out to the car and sees it open. And he thinks nothing of it, despite knowing he didn't open it. Logic would say, "Well someone else opened it."
Plot hole: Bond would not have had (nor taken himself) time to lay a complete and careful clown make-up while changing clothes in the circus trailer.
Plot hole: Following Glen's death, Nancy tells her father to come across the street in 20 minutes to catch Freddy. She then goes to her house, checks and sets her alarm clock, and proceeds to rig the entire house with booby traps, including filling a light bulb with the contents of several shotgun shells, and has a heart-to-heart talk with her inebriated mom. When she gets back to her room to go to sleep, she checks her clock again. The time on the clock has advanced only ten minutes, not nearly long enough for everything she did.
Plot hole: When Iris Henderson and her two friends arrive at the hotel, Iris orders dinner and asks that it be sent up to "our" room. The waiter arrives when the three are changing. But later, when it's time for bed, Iris says good night to her friends, who leave her alone in the room (as she must be for the sake of subsequent developments).
Plot hole: It has already been mentioned that a certain shot reveals that Sidney isn't wearing the bullet-proof vest when she should be. Further to this, most of the shots in the climax sequence make it impossible for her to be wearing one, as you can see the contours of her chest throughout. A bullet-proof vest would flatten the appearance of this.
Plot hole: The original ending planned was a massive tropical storm/water based chase scene. However, this was decided to be too expensive, and was switched for a cheaper, and some say weaker ending. Nonetheless, in Nicholas Cage's final speech, he says "I keep thinking about that tunnel, and what would have happened if I'd drowned." This makes no sense, given that in the new ending he came nowhere near a tunnel or drowning.
Plot hole: The suitcase with all the money is at the fake doctor guy. This makes absolutely no sense - it was given to the girl. Why would she hand it over to that guy when they could have done the splitting of the money right that night?
Plot hole: George Lebay says that his brother died "6 weeks ago" inside Christine and that's why he's selling it. Later that evening after Arnie leaves his house and goes to Darnell's, Will Darnell says he "knew a guy who owned a car like that" and "the bastard killed himself in it." If it's only been 6 weeks since his death, shouldn't Darnell have recognized the car? It's not like there were lots of red Plymouth Furies (custom order color) running around the small town, let alone the USA, even in 1978. (Also considering how production even had a hard time finding them for the movie).
Suggested correction: He says he knew a guy with a car like that. It doesn't have to be the same colour or even the same generation. Just a Plymouth Fury.
Darnell basically said he knew THE brother of Lebay, not just some guy who owned a similar car. Darnell described Lebay's brother based on the story. Again, it was him, not just some other guy.
Plot hole: In the first night that Nyah is in Ambrose's house she meets with Ethan outside the house and they talk for about 1 1/2 min. Then we find out "Ethan" was really Ambrose with one of those "high-tech" masks. My question...After being in bed with both, how come Nyah didn't recognise Ambrose is about 5 inches taller than Ethan?
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: It makes absolutely no sense that there would be over a dozen cops and soldiers in the lobby of the courthouse and leave only two cops to guard Lecter regardless that he was locked in the makeshift cell. Yes the plot needs a reason for him to easily escape but this still goes against every conceivable protocol for such a dangerous prisoner especially when there were dozens of armed personnel just in the scene alone when he was being transferred from the plane.
Plot hole: In the last car-chasing scene, the timekeeper had switched his car to chase them, then how could Justin Timberlake get the timekeeper's salary (a day's time) from a car that the timekeeper picked up from the streets?
Suggested correction: I think it is the car of another time keeper. Hence, it may have a time transfer system.