Some glaring plot holes...(SPOILERS)
1. Caul's character is secretive and very private. Yet he throws a party in his workspace, with all his sensitive secret equipment, and sleeps with a strange woman next to his latest project, allowing her to steal all his work.
2. Harrison Ford has been called the "gay lover" of the Director. But if this were true, then why would he want Caul to shut up about the murder in the end? Wouldn't he be out for blood against the couple?
3. Why did the director go to the hotel, when he knew the couple was planning something? In other words, if he thought they were just planning to have sex in the hotel, wouldn't red flags go up if one of them tried to invite him there?
After all, they had to "lure him" there, right? It is understandable that he would want to go to the hotel and "bust them", but if one of them invited him, he'd have to rethink what they meant by "do it". And being such a man surrounded by henchmen at his office, he'd certainly arrive with henchmen in a waiting car, and not just get murdered and have his body removed etc. without his men not knowing about it.
4. How is asphyxiation and stabbing consistent with wounds from a car crash?
5. How did the couple get the body out of the hotel without anyone noticing?
How did they clean it up so well?
6. Why did Harrison Ford's character insist on getting the recording so fast?
If it was so important to his boss/lover, the "Director", then why not just call him up and say, "This guy Caul won't hand over the tapes to me, can you talk to him?" Why follow him around and then hire some strange bimbo (who happens to already work for his competitor/colleague) to sleep with him ..in his shop! nonetheless..in the hopes of stealing the tape...when after all, one phone call from the director would have probably been enough to smooth Caul's fear that the tapes were going into the right hands? Because in the end, Ford and the Director are listening to the unedited tape right there, together, in front of Caul, so all the skullduggery was so unnecessary and distracting.
7. How did Harrison Ford's character read Caul's mind or pretend to know what he was thinking? First, about destroying the tapes (why would he make the assumption that Caul might want to destroy the tape? And why did he insist it was "dangerous"? ) Second, at the end he said "We know you know; don't do anything"? How does he know Caul knows anything? Sure, Ford's character said they were watching Caul, but even those closest to him couldn't figure out what he was thinking, so how could some stranger know?