Revealing mistake: When the camera moves into the "Seeing Stone" and pans up to reveal "the great eye," the entire tower was a miniature. It's not that noticeable, but what really makes it a mistake is the cotton balls used to make smoke on the smaller towers leading up to the big one. (It sticks out so obviously that one must ask, why did they CG the orcs at the bottom of the miniature, but use cotton balls for the smoke instead of CGing it?)
Revealing mistake: When Sam is running up the steps to stop Frodo from putting on the Ring in Osgiliath, you can see when he puts his right foot on the stair the "fake foot" toes slam into the stair and bend to a point which is impossible to achieve with a real foot.
Revealing mistake: In some shots you can tell that they used children or small people, for Frodo and Sam. Mostly, you can tell when they're shown from behind, in the company of tall men. You can also tell, from the slightly different hairstyles.
Revealing mistake: When Aragorn tracks Merry and Pippin near the beginning of the movie, after meeting Eomer, the trio stops at the border of Fangorn forest and you can see in this closeup that it's the scale double Brett portraying Gimli, not John Rhys-Davies.
Revealing mistake: In the aerial shot approaching the Horse Kings village the banners are flapping the wrong way and the chimney smoke is going into the chimney, instead of out, revealing that it was shown in reverse.
Suggested correction: Which scene is that? I couldn't find it anywhere.
It's the scene where Eowyn exits the door angrily and walks towards the fire circle thinking, in the trailer she's on the left of the screen but in the movie she's on the right.
Revealing mistake: Gollum is leading Frodo and Sam through the Dead Marshes, towards Mordor. When Gollum runs across the first bit of the swamp, he treads into water; but the water does not move, nor does Gollum act like he has tread in water.
Revealing mistake: As Aragorn, Legolas and Gimli gear up for the battle of Helm's Deep in the Keep, Gimli puts on chainmail. After he says it's too tight in the chest, you see a back shot of Gimli standing facing Aragorn and Legolas. This man is obviously a scale double, as the body and posture are wrong.
Revealing mistake: When Theoden says, "They will break upon this fortress like water on rock," the camera is in a crane shot which slowly creeps up, becoming a medium close-up of Aragorn. As the camera flies over the front wall of Helm's Deep in the shot where Theoden delivers his line, look down into the deepest level of the castle towards the left of the screen. Rohan citizens are bustling and moving. If you watch closely, you can see the lowest level of the castle jump and shake in the shot. This is because that lowest level wasn't there in reality and it was added in the computer. (Probably can be seen only in the Widescreen version).