Continuity mistake: As Harrison Ford hands the Captain a picture of Colonel Kurtz note the salt shaker and spoons to the right of his plate change. The salt shaker disappears and the spoons are suddenly side-by-side when the Captain places the photo on the table. (00:12:30)
Continuity mistake: After the gentleman in the tan jacket says, "The white left, but the yellow stays". Look closely at the plate that he drops the egg into as the two pieces of bread change into pastry between shots. (02:07:25)
Continuity mistake: As Lance dances around with the purple smoke canister there's nothing in front of the helm of the boat under the radar dome. Later as the rocket attack that kills Clean starts a helmet appears there. (01:51:30)
Visible crew/equipment: Captain Willard is on the right side of his bed dancing and he sticks his right fist towards the camera. Watch the bedspread closely as he pulls his fist back and you can see the shadow of the camera moving on the bedspread. (00:06:50)
Audio problem: On the beach Colonel Kilgore takes the radio phone from one of his soldiers and calls in the napalm attack on Vin Din Dop. If you look closely at his lips they do not go along with what he's saying. This happens again two shots later when he sends the Vietnamese woman and her baby to the hospital by helicopter. (00:47:25)
Audio problem: Approaching Kurtz' compound Lance starts drumming on two tin cans and if you listen closely they get the overdub wrong. At first we hear two distinct pitches, which are the actual sounds, picked up by the microphone but the last time he hits it we hear a third higher pitch which was overdubbed. There are only two cans not three and he doesn't change the way he's holding them therefore you can only have a maximum of two audible pitches. (02:29:05)
Continuity mistake: As Captain Willard stands in front of him the shrunken head hanging off Lieutenant Colby's rifle is not this same one we saw several seconds ago when the captain first set eyes on him. The second one has thicker darker hair and is attached to the rifle differently. (02:33:00)
Continuity mistake: When Captain Willard shakes Chef's head off of his lap it falls into the mud face down and in the dark. In the next shot the head is face up and in the light. (02:47:25)
Continuity mistake: The blood and scrapes on Captain Willard's nose disappear as he speaks to Dennis Hopper from the cage. (02:43:30 - 02:45:00)
Continuity mistake: As the little French boy goes to kiss Hubert de Marais the man wearing a tan jacket in the center of the screen goes from looking to his right to looking at his food between shots. (02:03:00)
Factual error: The date on the top of Chef's letter from Eva says, "Sept" with the year conveniently whited out. If the letter was written in September of 1969 she couldn't have known about Manson who wasn't arrested until December 3, 1969. This also dates the movie as taking place sometime in 1970. (01:50:50)
Visible crew/equipment: Just before the Playboy helicopter takes off from the stage the first stuntman who hangs off the skid runs up, taps on the window to signal the pilot, then reaches down for several seconds as he attaches a cable to himself. You can see the second stuntman as he holds onto this cable with his right hand when he pulls the first stuntman's pants down. (01:10:20)
Continuity mistake: Chief Phillips gives the helm of the boat over to Chef as Clean continues with his story. Lance takes the plastic covering off of the top water-ski then in the next shot it's covered again then uncovered in the shot after that. (01:12:50)
Continuity mistake: Before they leave the Do Lung Bridge Captain Willard yells to Chief Phillips, "Just get us up river". When he does this he's sitting down but in the next shot as the boat pulls out he's standing up. (01:48:15)
Revealing mistake: When Marlon Brando throws Chef's head to Martin Sheen, you can see Chef's head breathing in the close up shots.
Continuity mistake: Chef says, "I gotta remember, never get out of the boat" as he sits in front of Chief Phillips on the starboard side of the boat. In the next shot as they pull away from the tree they've been hiding under he's walking around on the other side of the boat. (00:59:30)
Continuity mistake: During the arrow attack Chief Phillips grabs a machine gun and starts shooting. At first he and Chef's guns are both pointing in the same direction, starboard. In the next shot one gun is facing one way and the other is facing the opposite way. (02:22:15)
Continuity mistake: The gentleman in the tan jacket to the left of Roxanne is eating when Hubert says, "You don't understand our mentality". In the next shot he's reaching over and pouring a glass of wine for her. (02:05:20)
Continuity mistake: The gentleman sitting next to Roxanne in the tan jacket gets up and says, "Look, Captain," and Roxanne reaches over with her right hand as she holds her cigar in her left. In the next shot she's sitting with both hands on the table and the cigar in her right hand. (02:07:20)
Continuity mistake: As Chief Phillips orders Chef to, "Check what's in that vegetable basket," the Vietnamese woman runs past and hands him papers that he takes with his right hand. In the next shot as he pushes the woman the papers are in his left hand. (01:36:25)
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