Continuity mistake: In the scene where Jack Black and Adrian Brody are talking on the boat (as it's getting ready to leave), when the camera is focused on Jack, the cityscape behind him (through the window) is moving (as if the boat has started moving), but when it focuses on Adrian, the cityscape behind him (through the window) is not moving.
Continuity mistake: When Ann is about to steal the apple, she picks up a different apple first. When she is about to put it back, the angle of the apple in her hand changes. Watch the apple stalk and you can see it.
Continuity mistake: When Ann is dancing in New York while King Kong is enchained, her hair is straight and then curly in the ends. But when she goes out in the streets and sees the Kong poster her hair is wavy. When she finally meets Kong again her hair is back to straight and curly.
Continuity mistake: In the scene where the boat is leaving NYC and the camera is panning around it - the smoke from the ship "follows" the camera by always pointing to the right relative to the camera view; even though it should be trailing backwards, opposite of the ship's direction.
Continuity mistake: After the screening of Carl's movie he walks down and says "The script has been re-written", while he has his left hand up by his waist. When it cuts his left hand is hanging down.
Continuity mistake: While telling Carl about the shipwreck sailor the crew of the venture picked up on an earlier cruise, Lumpy keeps whittling on a piece of scrimshaw. He continues to do so when Carl is about to leave the galley. In the next shot, when Carl turns back to give a reply, Lumpy's arms are suddenly lowered at his side.
Continuity mistake: During the whole film, even though Ann is thrown about and man-handled by Kong, as well as sliding down rock and cliffs in bare feet, and falling over numerous times to escape the many creatures and dinosaurs, she ends up with virtually no marks or scratches on her body. Her dress is dirty, but that is about it. Her hair also stays reasonably in place. Surely she would have been scratched and bruised all over her legs and arms from the trauma.
Continuity mistake: In the scene where the movie star is trying to talk them into giving up he has a rope slung around his chest over one shoulder. He never takes it off, but when he leaves he no longer has it, and Adrian Brody is holding it.
Continuity mistake: When the main characters first arrive on the island and are attacked by the natives, one of the natives attempts to decapitate Carl but Englehorn arrives at the last minute and saves him by shooting the native three times. As he is falling, it is very noticeable that there is not a scratch on him. He never bleeds at all, there is not even an entrance hole for any of the bullets.
Continuity mistake: When Kong has grabbed Hayes, he tells the rest of them to get out of there. As he says "Do as I say", his gun is pointing at Kong. When it cuts he suddenly has his other hand on the gun cocking it.
Continuity mistake: When the old man says he is moving back to Chicago, Ann hugs him and place her hand around him right below his neck. When it cuts her hand is lower down on his back.
Continuity mistake: Aboard the Venture, when Ann runs into Jack with her "good legs" she has a towel on her shoulder, which changes position until she goes to her cabin.
Continuity mistake: When Ann is caught stealing the apple, Carl pulls up a coin saying "Excuse me. Ma'am, I think you dropped this". The way he holds the coin differs in the next shot.
Continuity mistake: When the sound engineer says "We're gonna have the ship's engines all over the dialogues", he has his left hand to his headphones. When it cuts his hand is gone, but in the next shot his hand is back on the headphones.
Continuity mistake: Jack and Carl are in Carl's stateroom. Carl opens the crate of whiskey, takes out a bottle and puts it down. The bottle then turns itself around so the label's sometimes visible, sometimes not.
Continuity mistake: In the scene where Ann is unconscious, Kong puts Ann on the ground and she is lying on her arms. When it cuts to the shot when he begins poking her, one of her arms is stretched out.
Continuity mistake: When Ann and Kong are on top of the Empire State Building near the very end, he sets her down on top as he grows weaker. She begins to stand, pulling herself up on his fingers, the shot cuts and she is standing but his hand is now out of place back towards his body, not near Ann where it should be.
Continuity mistake: After the dinosaurs fight against Kong, Dwan falls on a lake and runs away while staring at the dinosaur. Several bangs of hair cover her forehead. A shot later, when King shows up her forehead is hair-free.
Continuity mistake: In the scene of the ship and movie crew trying to escape from Kong, Kong smacks the bow of the boat, sending Denham into the water in the long shot, but the next close up shot it's Denham splashing into the water again.
Continuity mistake: When Anne is on the rotten tree branch, trying to escape the giant lizard, there is a large black leaf on her chest, but, in the next shot, it's gone.
Answer: They scared them off with their guns. In the scene where they capture Ann to sacrifice her to Kong, Denham and his men come to rescue her and when they start shooting the natives hide. It's never fully explained but the most likely answer is that they are too scared and have even moved villages or are just hiding really well.