Continuity mistake: They took the flag from the PBR (which is removed from the roof of the boat the next time we see it) to cover Clean's body at burial. It's not the same flag, the last red stripe on the bottom of the PBR's flag is torn off as we see at the French Plantation dock. The flag on Clean's body has the last red stripe and also has a shorter white stripe on it's bottom. There's no indication that there is more than one flag on the PBR (redux version). (02:00:05)
Continuity mistake: When Captain Willard runs into the photographer when he reaches Kutz's compound the scene keeps jumping back and fourth between the two characters as they walk around. The photographer is wearing a red headband. As the film shots keep jumping back and fourth between the two characters the headband changes from being folded flat to being rolled up across his brow.
Continuity mistake: Several different boats are used in this movie as "PBR Street Gang" and they are almost duplicates of each other. In the scene where Clean is killed look at the handrail on the port side that extends from the rear of the roof towards the front of the boat. The last section is kinked up at a 45-degree angle where it's attached to the roof. Two minutes later we see a wide shot of a different PBR which has a gentle bend in this piece of metal rather than the abrupt bend on the other boat. (01:52:00 - 01:54:05)
Audio problem: In the first aerial shot of the schoolyard the closed captioning reads, "this should make everything burn" but if you listen closely what the pilot is actually saying is, "can somebody cover that downed bird". Also the helicopter he's talking about hasn't been shot down yet. (00:40:20)
Continuity mistake: As Chef tries to put the fire out with the fire extinguisher Captain Willard is hanging over the side of the boat with Clean as they try to escape the flames. In the next shot and as chief Phillips walks around him he's behind the helm of the boat near the Playboy picture that Chef taped up. (01:16:50)