Continuity mistake: Colonel Kurtz sits reading articles from Time magazine facing the captain and the sun is behind him shining right into the doorway. When we first see Captain Willard locked up in this room he's facing Kurtz and the beams of sunlight are coming in from his left, which is 180 degrees in the opposite direction from the shots of the colonel.
Continuity mistake: Captain Willard and the men get off the PBR and walk to their right about 30 feet in the direction of the hut that is destroyed by the boat with the teeth painted on it. In the next shot when they run into Francis Ford Copola they're back to where they started as we see the boat directly behind them.
Continuity mistake: After Captain Willard looks at the picture of Colonel Kurtz being decorated by General Westmorland, they're all startled by the "Arc light" B-52 strike, note the rear machine gun is pointing forward and a helmet is hanging from the middle machine gun. In the next shot the rear machine gun is pointing aft and the helmet is now gone.