Audio problem: After the scene where the men had to fight off the giant bugs, there is a wide shot where the men can be seen being helped out of the pit by the captain and a few extra crewmembers. The captain is shouting something, however, if you look closely, his mouth is not in sync with what he is saying.
Audio problem: When Carl tells Preston to show Ann on board the ship he says something like, "Hello, Miss Darrow, I'm Mr. Denham's assistant." His lips aren't properly synchronized with the dialogue when he says this.
Audio problem: When the ladder Ann was standing on hits the ridgy part of the Empire State Building there is no loud crash.
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.