Plot hole: When Carl is helping Molly out after Sam dies, he manages to find Sam's address book in a box, which he needs to launder the money at the bank. So why does he need to convince Molly to take a walk outside so Willie can break in the apartment and steal it? Carl knows which box the address book is in, and could have easily stolen it earlier when Molly was not in the apartment.
Suggested correction: Carl couldn't have stolen the address book earlier; it's possible he didn't know where it was, and he had to use the visit as an excuse, or it's possible he knew where it was but was thwarted because Molly wouldn't ever give him a chance to steal it, since she wasn't leaving the apartment. And he couldn't steal it later, because Molly wasn't leaving the apartment. His only chance was to lure Molly away so that Willy could come in and get it.
Since he worked at the bank with Sam, he could, without raising any red flags, simply ask to copy a few numbers from the book. Also, while he was walking with Molly, how did he contact Willie and tell him to go in? They didn't have texting back then. And how did he not know Molly had come back, if she had been walking with him? Other than the obvious, fourth-wall-breaking excuse that he didn't want us to know he was the villain yet.
Plot hole: How does Agent Lahiri know that you needed to raise the pylons before it was possible to make the cross bow shot the boys needed to unlock the house in Amsterdam? Additionally, those pylons would not be accessible through water as they are planted in mud under the foundation of the building, not water.
Plot hole: When Gawain is repairing the hole in the vault wall, a security camera is visible in the top corner in the room.
Plot hole: Cindy manages to pick Crisp out of a line-up even though she was hidden in a box and didn't see him, she only heard his voice. But even with that, he isn't asked to speak during the line-up.
Plot hole: In the opening of the film, some of the characters are flipping through a scrapbook they've made documenting Elle's experiences in the first film. The problem is that many of the pictures are of moments when no photos were taken, so how did they get the pictures to put in the scrapbook?
Plot hole: When the students are breaking into ETS, they take great care to avoid the security cameras in the lobby; donning masks, crawling on the ground, etc. Yet a bit later, two of them go back to guard the same lobby, they are seen walking around and sitting on the desk that they so carefully crawled past earlier.
Plot hole: The Hillbillies take a "short cut" to catch up with the guys after they are taken in by Burt Reynolds. However, the guys get a chance to sleep comfortably until morning before being confronted by them. (01:12:10)
Plot hole: It takes less than 3 minutes to fill the house with water using a mere garden hose? I mean come on...
Plot hole: Michael McKean quits pursuing Beldar and approximately 15 years pass as indicated by Connie growing up, yet when you see McKean again and his assistant, they have not aged at all.
Plot hole: While planting the suicide gear in the bathroom before Buckley comes in, Cooper tells Josh to tie the rope into a noose as they go to hide in the shower. Josh replies that he doesn't even know how to tie a noose. He must be a quick study, because in the 45 seconds or so that it would have taken Buckley to relieve himself and wash his hands, Josh has tied a perfect noose. (01:03:55)
Plot hole: The policeman survives a frontal crash into the hillbilly's truck at full speed without as much a scratch. (00:24:40)
Plot hole: Edward Lionheart severs the head of theater critic Horace Sprout while Sprout and his wife are asleep. (Lionheart gave them both a knockout injection). Sprout's wife (and his maid)discover the severed head in the morning, and both scream and faint. But in the next scene, critic Perry Devlin retrieves his morning newspaper and then reaches for his bottle of milk, only to find Sprout's head perched on the milk bottle. How did the head get from Sprout's house to Devlin's place?
Plot hole: When Hugh is walking near the park gate, he should have seen Marcus. Marcus was on the same side of the post as Will was.
Plot hole: The fact that David becomes conscious after being hit and left back is dramatically fine but there is no aftermath - he misses to finish dealing with Ali and friends at that point.
Plot hole: At the end of the film the boss says that he and Miss Fitzgerald are going to go on holiday together to Paris (talking about the actual city, not the secret code they have invented). However, the film is set in 1940 and Paris would have been an unusual place to take a holiday at this time, considering France was in the middle of a war... Pretty dangerous for civilians even though America was still neutral at the time.