Continuity mistake: On the cliff where Ann is entertaining King Kong by dancing, juggling, doing flips, etc. her face goes from dirty, to clean, to dirty, and back to clean between shots.
Continuity mistake: At the end of the chase through the streets of NYC, Kong stops the yellow cab with a "karate chop" to the front-end, which sends the car tumbling high into the air through a complete somersault before it lands back down. Actually, Kong's hand is still half way down and nowhere near touching any portion of the vehicle when its rear-end gets lifted.
Continuity mistake: When Jack is rescuing Ann she has two cuts above her right eyebrow, the smaller cut changes positions and disappears/reappears in different shots.
Continuity mistake: When Kong falls through a portion of the circular observation deck at the top of the skyscraper, he crushes the metal siding as well as one of the metal girders, making a large hole. When he puts Ann inside through the hole, the metal girders are now all undamaged. You can tell that this is the same hole because the camera moves around the entire building in the next shot and there are no other large holes.
Continuity mistake: Shortly after Kong realizes he's been shot and gets blood on his fingers by touching the bloody hole in his chest, in subsequent scenes his chest has no puckered indentation and is unblemished but for minimal straight-line scars.
Continuity mistake: When Carl falls at the beginning of the brontosaurs chase we see that he is only just in front of the brontosaurs so when he fell he should have been crushed straight away but he isn't. Jack then runs to help him and we see that the brontosaurs only need another step or 2 (which would take 1 or 2 seconds) before they reach Carl and Jack. Carl gets up and argues with Jack for 5 seconds or so by which time they should have been crushed. They then run and there is a far off shot showing the brontosaurs back where they were at the start again.
Continuity mistake: Ann is soaking wet when she is being led through the natives. When she gets to the top of the wall she's dry.
Continuity mistake: When the Skull Island natives are holding Ann's arms as the old native taunts her, their grip on Ann's arms and sleeves differ between front and back shots.
Continuity mistake: When Carl and his assistant are driving in the cab discussing who to fill in on the female role, you can see that they pass a tram on their left side. When it cuts the cab is right in front of the tram rather than to its right.
Continuity mistake: When Carl is convincing Ann inside the diner, after she stands up and Carl convinces her to accept the role, there's a waitress behind Carl about to walk towards her. A split second later, while Carl says "she's the saddest girl he's ever met", the waitress appears 12 feet away, and is now behind Ann way at the end of the diner.
Continuity mistake: Kong continues to change size during the movie. The most obvious way to notice this is when his hands are near Ann. When Kong first finds Ann in NY, his hands are 3/4 the size they are immediately after when he picks her up.
Continuity mistake: When it cuts to the filming of the first take between Ann and Bruce on the ship, it shows Jack standing on the right side of the picture, about a feet away from the wall of the ship. When it cuts to a close-up of Jack, he is suddenly leaning against the wall.
Continuity mistake: When Kong is about to fight the last Rex, Ann begins to back under his arms. In a distance shot we see that she is already a fair distance behind his arms, underneath him. Cut to Kong noticing this, then cut back to a back shot of Ann backing under and she has not even reached his arms yet.
Continuity mistake: When Carl speaks with Hayes and Lumpy about their destination, while aboard the Venture, the towel rags hanging on a line behind Carl change between shots.
Continuity mistake: Before going on board the ship, Captain Englehorn asks Ann if she is nervous while he lights his cigarette. You can see his cigarette remains in his mouth, but when it cuts it's no longer in his mouth.
Continuity mistake: When Kong is at the top of the Empire State building we see Ann start to climb the ladder and she is only a few rungs up when the camera view changes. When it cuts back to her, she is still climbing those first few rungs.
Continuity mistake: In a scene at the very top of the Empire State Building, Ann hugs Kong's left arm. In the very next shot, she is standing right in front of Kong, between both of his arms.
Continuity mistake: When Ann and Jack are about to kiss the first time, there is a close-up of Ann's face. When it cuts Jack's hand suddenly appears on her face.
Continuity mistake: After Ann and Carl arrive at the docks, as she stands beside the Venture her coat collar is flipped up, then turned down and back up between shots.
Continuity mistake: When Carl steps out of the room after screening his movie he doesn't cast any shadow on the door behind him. When it cuts his shadow suddenly appear on the door.
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.