Continuity mistake: When Willard has a severed head dropped on his lap, the stump is clean and flat like it was sliced by a samurai sword. When the head falls to the ground, the stump is bumpy and ragged like it was hacked with an ax.
Continuity mistake: As Colonel Kurtz reads his poetry out loud we see Dennis Hopper gesturing with both hands as he speaks with the captain. When the colonel gets mad and throws the bowl of bananas at them Dennis Hopper is holding his camera in his left hand. His bandana is also rolled up differently with the corner sticking up in one shot and down in the other. (02:56:20)
Continuity mistake: As Captain Willard tries to get Lance away from Colonel Kilgore the band-aid on his right cheek angles upward as it nears his eye. Later we see it up close as they pull him into the boat with the surfboard and it does not angle upward but goes straight across his face. (00:50:40 - 00:51:45)
Continuity mistake: As they all read their mail from home Lance ignites a canister of purple smoke and it's sunset. In the next shot of Clean grabbing his tape recorder it's the afternoon and the sun isn't even shining. (01:50:55)
Other mistake: Captain Willard reads to himself from Colonel Kurtz' paper titled, "Commitment and Counterinsurgency". We see a close-up of the page that he's reading from which is fine until he reads, "our conduct of the war will gain only impotence". Everything else he reads is not on the page. (01:15:35)
Audio problem: As they approach the Do Lung Bridge Lance tells Chef that he dropped a tub of acid and Chef says, "far out " but if you look at his lips he's not saying anything at all. (01:40:50)
Other mistake: After we see Chief Phillips break up the fight between Clean, Lance and Chef they show a close-up of the Playboy Bunny's helicopter. It's pouring down but there's no water running off the helicopter or its windows. (01:25:40)
Visible crew/equipment: After Clean is killed in the rocket attack there are several shots where the camera crew films the front of the PBR as it approaches them. The spray and turbulence from their boat in front of the PBR can be seen in all of these shots. (01:52:20)
Continuity mistake: As they approached the French plantation the partially crushed fuel drum on the back the PBR that we saw after Clean was shot, has been replaced with one that is only slightly dented. (01:56:15)
Continuity mistake: As they depart from the USO show at Hau Phat Chef shows everyone his picture of Miss December and there's a helmet hanging on a poll in the rear of the boat with the top facing Chief Phillips. Each time we see this helmet in the next few shots it moves sometimes facing the back of the boat and sometimes facing the front. (01:11:55)
Continuity mistake: As they approached the French plantation there are two distinct shots of this area, one is from further back then ten seconds later there's a close-up. The clouds in the background are entirely different in these two shots and the clouds change again when the Frenchmen show up. (01:55:50 - 01:59:20)
Continuity mistake: As Roxanne sits down at the table Captain Willard looks at Hubert de Marais. In the next shot he's smiling and looking at Roxanne. (02:04:10)
Continuity mistake: As Captain Willard takes a smoke, the shadow of the pipe is on Roxanne's face but in the next shot as she looks at him the pipe's shadow has disappeared. (02:17:30)
Audio problem: As they lie there in bed Roxanne says, "you are alive captain" and you can only see the side of her face. Her jaw is not moving and if you look closely at her face, all she's doing is returning the captain's smile, not talking. (02:18:10)
Continuity mistake: As Roxanne unties the curtains around the bed the scarves draped over the light on the left of Captain Willard are not the same ones we just saw in a previous shot as the captain took a smoke from the pipe. The ones before were red and yellow but now the middle one is primarily green. (02:19:05)
Continuity mistake: As he says, "so when you ask me why we want to stay here, Captain" Hubert's face and jacket go from being in the light to being in a shadow between shots. (02:21:30)
Continuity mistake: On the beach Colonel Kilgore says to one of his soldiers, "what do you know about surfing major, you're from New Jersey" look closely at the Vietnamese prisoners walking on the opposite side of the beach. They're always walking from left to right but several times in this scene they change their starting position from further down the beach (left of screen). (00:45:50)
Continuity mistake: As Captain Willard takes a smoke from Roxanne's pipe the pillow he's lying on is light green. Later after they're finished as he lies on his back the pillow is now light red. (02:17:20)
Continuity mistake: After Chief Phillips falls to the floor of the boat Captain Willard kneels down to try to help him. Look closely at Phillips' left hand, there's blood dripping on his knuckle. In the next shot when he grabs the captain around the throat there is no blood on his left hand. (02:23:05)
Continuity mistake: As they all sit on the boat and listen to the "Arc light" B-52 strike Lance is sunbathing in direct sunlight. In the next shot he's in the shadow of the roof of the boat as he gets up and says "there they are". (00:24:15)
Chosen answer: Kurtz was protected by political connections and his military record from being relieved of command, and the Montagnard people whose village he was in were considered American allies, so they couldn't just send a force in to kill him or relieve him of command, but an individual assassin. (The US Government's "official" policy is that they do not engage in assassination, which is why "this mission does not exist, nor will it ever exist").
Captain Defenestrator