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: The assassin cuts a hole in the glass to kill the Federation president. But with the size of the hole and the placement of the scope on the phaser rifle, the assassin would not have been able to see out of the hole.
Plot hole: When Frank gets the phone call that Bobby has been shot, all that is said is that Bobby has been shot on the street in Italian. They never said Richie shot him.
Plot hole: Spoiler Warning. It turns out that Dan Merrick is actually Jack Stanton after a whole lot of reconstructive surgery to make him look like Dan Merrick. Everything is believable except that he has Dan Merrick's voice as well. He should have Jack Stanton's voice.
Plot hole: At the bar shootout where everyone except Marlboro and Harley are murdered, the two jump through the window, over the fence, into the airport, and into an airplane luggage compartment. They would have been caught by security. The missing, and dead, airport worker would have been missed and searched for, the gunfire would have attracted attention, and the police would have been called. They never would have left the airport.
Plot hole: Cady's plan to get revenge on Bowden includes raping and assaulting Lori. This part of the plan, however, hinges on Lori not reporting Cady to the police, which he had no way of knowing that she wouldn't. If she reported him, the investigation would have created huge problems for Cady. He bit off a chunk of her face, so the wound could have been matched to his teeth, as well the chunk of skin he bit off and spit out most likely would have had traces of his saliva on it. Not to mention evidence that could have been gathered from a rape kit and eyewitnesses that could have placed Cady at the bar with Lori beforehand (the bartender, for example). In all likelihood, he would have been arrested, tried and convicted. Lucky for him, Lori was too ashamed to report the incident.
Suggested correction: Luck didn't come into it. Cady specifically targeted her because of her connection to Bowden, and took the calculated risk that she would not want her sexual history being dragged in front of a court and all her co-workers. This ties into Cady's motive for wanting revenge on Bowden in the first place, as he had suppressed similar evidence in Cady's original case. Also, Cady is a very unhinged individual; the submitter's opinion on how sensible his actions are does not make them a plot hole.
Plot hole: Laura rents a nice, large house, furnished with everything she needs, using a fake name, no job, no financial history, has no current bank account or credit cards or any references. She merely hands cash to the agent. She later lands a job without proof of identity, citizenship or residency (legally required), and has no references, no credible work history, or a SSN#. Laura is resourceful, but would lack the means to obtain a convincing fake identity and other false documentation.
Suggested correction: You don't have to be a citizen to work.
You do need an ID, but you don't need to be a citizen.
You need to be a U.S. citizen, a "legal" resident, or have a specific type of work visa to be legally employed in this country. You also need an identity for renting a house or apartment and a prospective tenant doesn't just hand over a large sum of cash for the rent/damage deposit without immediately getting a receipt, while standing on the porch, and not first filling out paperwork.
Plot hole: When the police chief asks Joe 'where's the briefcase they were telling me about?' Joe tells him to look in the back seat of the white BMW. There are a couple of problems with this. First, the police chief is looking for a case with a bomb in it, because he received a phone call from the guy who had his BMW stolen. Even if he knew about the money, which is unlikely, the police chief has no way of knowing that the case he is about to open is not a bomb, since no-one saw Marcone steal the case with the bomb in it. Yet he opens it without calling the bomb squad. Second, Joe saw Jimmy put the case with the bomb in the back seat, so why doesn't he warn the police chief about it? (01:35:00)
Plot hole: No amusement park ride company would ever produce a prop scythe that was as sharp as depicted in the movie.
Plot hole: The pipe bomb that Maggie uses to kill Freddy is the same one that was found in Spencer's room earlier in the film. It's already been established that Freddy was erasing the people he's been killing from existence, so that pipe bomb wouldn't be there to use on Freddy.