Revealing mistake: When Kong first shows up to take Dwan away, he roars and pounds his chest. As he does so, the breastplate in Rick Baker's costume vibrates visibly in a way that a flesh-and-blood chest wouldn't.
Factual error: How does Kong return a radar signal? If organic material is suddenly detectable by ship borne radar, why isn't it picking up the trees and other animals? Did someone invent gorilla-detecting radar?
Factual error: When Kong falls in the pit containing the chloroform and passes out, you can see some of the boat crew members walk into the chloroform cloud to look in the pit. Wouldn't they pass out also?
Revealing mistake: Near the end Kong rolls off the top of the World Trade tower. It cuts to a shot from the ground looking straight up toward the top with Kong falling downward. For a fraction of a second there is no image of Kong composited into the shot: first there's just buildings, then suddenly Kong appears from nowhere in midair.
Continuity mistake: When the group of natives has discovered the Petrox crew and begins approaching them, a closeup shows Dwan moving from a crouching to a standing position and nervously taking a few steps back to stand behind Jack. The camera then switches to a long shot and she again stands up and moves behind Jack.
Continuity mistake: At the beginning when Dwan is tied to the podium and waiting for Kong she looks up and the trees are moving with Kong's presence. Then we see Kong approaching through the woods from a distance.
Continuity mistake: At the top of the twin towers, Kong hits the same chopper twice.
Continuity mistake: When Jeff Bridges and the girl escape while Kong is fighting the snake, they jump into the water and get soaked but a few moments later their clothes and hair are completely dry.