Plot hole: In the scene where William takes Murron for their initial ride, he shows up in pouring rain, yet all further shots show the two of them totally dry. The tone of her mother's voice when they get back suggests they did not spend the night together, and the whole sequence appeared in a couple hours. They could not have gone from soaking-wet to bone-dry that fast.
Plot hole: When Bo-Tat is purchased the Village Elder insists that Lihn go with Bo-Tat, it is CLEARLY established at this time that A) Lihn is an orphan and B) his parents were both killed in the war. For two-thirds of the movie Capt. Doyle repeatedly comments that Lihn can't be trusted because we don't know who (NVA or USA) killed his parents. There is no possible way that Spc.5 Farley wouldn't know this. However, halfway through the movie (on the river boat) he asks Lihn where his parents are and how they died. He couldn't possibly be ignorant of this, since he took part in at least two of the prior conversations.