Some problems with the movie... (spoilers)
The shoddy screenplay which shows most of its faults when it comes to characters motivations. There is just too much dumb behavior. Characters too often act the way the screenwriter needs them to act. Some actions can almost be considered plot holes (Rourke's casual walk into a suspicious building to get the case at the end).
The supposed fact that some scenes where cut. Mimi Rogers had more scenes and I'm sure the two Rourke's female helpers were suppose to show up again at some point. There's also a noticeable lack of M. Emmet Walsh after the first 15 minutes but that might just be stunt casting. The Mimi scenes were probably suppose to show Dafoe's boredom with his peaceful life in general which would explain why he decides to play an agent. Other scenes were probably cut to make the plot less complicated.
If these were kept the first complaint would probably have slightly less merit.
Rourke's character should have been ex CIA. A dirty secret. That would make some sense. The way his character was handled here makes the conspiratorial message seem forced and tacked on. CIA agents can simply kill other government agents as they please? And the heads of CIA allow it instead of just telling the FBI to pull their men back. Sure...
If Rourke is CIA, why doesn't he have the additional 250k? He works on a black ops budget or something?
Jackson takes the money and doesn't think FBI will look for the missing evidence? Ok. Maybe he plans to kill the courier and blame the theft on him. But he needs Bob alive in order to get the money from the weapons sale. And how long would that take? Weeks? That's A LOT of time for him to risk being discovered.
The guy who's monitoring Dafoe's room for Jackson. He gets beaten up and thrown into Jackson's room by Defoe. When Jackson confesses everything, the guy IS STILL IN THE ROOM. And we never see him again. What? Did Jackson kill him too? Did the guy just leave and decide to keep quiet?
And what happened to the FBI agents' bodies? Did Dafoe bury them? Did he call the cops? Even if they are dead, the first person the NEXT FBI batch sent to find these two will try to find is him since the missing/dead agents were there to determine the level of Dafoe's involvement in evidence theft in the first place. So how is he off the hook again? They have found the money, Rourke and Jackson. So? Jackson can still lie he was kidnapped by crazed Dafoe who send Rourke after him. Not to mention that there's nothing in Jackson's case but sand. There's no evidence that he's the killer or involved.