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: 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: How was Dolph able to start the car outside Yoshida's house after rescuing Tia? He didn't have a set of keys to that car, and he didn't hotwire it, so how did he get it started so fast, or at all for that matter?