Revealing mistake: When Jack starts walking on the log, there are square chalk T-marks painted on it to point out where he must step, which disappear in the overhead shot.
Revealing mistake: When Kong arrives at the top of the tower, his foot clips through the railing footage.
Revealing mistake: The flamethrower scorches Kong, who is behind an antenna. However, the antenna remains perfect, revealing it is a projection.
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.
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.

Revealing mistake: When Kong fights against the helicopters, the real helicopters have red and yellow lights all over, but the miniature ones have just a couple, revealing the FX trick.

Revealing mistake: When Kong grabs the subway car and throws it away, the lower part of the car is a blatant miniature model with no cables and no wheels.
Revealing mistake: When Kong picks up the subway car packed with people, in the wide shots, one can see it's empty.

Revealing mistake: When Kong pops out of the EL tracks and extends his hand, the glove is noticeably cracked, and the stuffing is coming out.

Revealing mistake: When Kong is atop the Twin Tower and throws objects to the soldiers below, check the last one: there's a blatant metal lid on the set ahead in the very same spot where an explosion occurs seconds later, most surely where the pyrotechnics were hidden.

Revealing mistake: When Kong is being burnt with the flamethrower, the flames have a clear clean cut on the left edge, revealing where the composite image was placed. In some shots, you can see the whole outline of the pasted image.

Revealing mistake: When Kong climbs up the Twin Tower, Dwan is replaced with a blatant doll.

Revealing mistake: After Kong takes Dwan out of the water, she is replaced with an unrealistic doll.

Revealing mistake: In the wide shots of Kong carrying Dwan around the barren lands, she is replaced by an obvious doll with stiff hair and unrealistic short arms.