Continuity mistake: Merry and Pippin were bound when taken by the Uruk-hai, and the bonds weren't cut until after they managed to escape during the fight. Yet, when the horse almost crashed down on Pippin, he had his arms spread out up near his face, not bound, even though they weren't cut until later. In the next shot, his hands are bound again.
Continuity mistake: At Henneth Annun, Sam suggests to Frodo to use the Ring to escape. Frodo and Sam are sitting in front of three barrels and also in the room are sacks, a crate and candles burning behind them. When Faramir arrives, Frodo and Sam are now sitting on blankets, there are no barrels in sight, the walls are different, there is an extra crate, with food on one and the candles are grouped differently.
Other mistake: When Eomer is mounting his horse after giving Aragorn, Legolas and Gimli the two horses, you can see his sword falling out of its sheath.
Continuity mistake: Gimli is lying with his face under the water, after jumping off the Deeping Wall and landing on the Uruk-hai. In the close-up, the right arm that grabs Gimli's shoulder to help him out of the water is Legolas' right arm. Yet, in the wide shot, suddenly it is Aragorn helping Gimli to his feet, not Legolas.
Revealing mistake: Just as Gandalf and the Rohirrim are riding into the Uruk-hai and they clash, go slowly, frame by frame. Legolas will be on the right of the screen. Keep going frame by frame. You'll soon see a few pretty clear frames of Arwen with her sword, on her white horse. She's sitting to the right of Legolas. Her long hair is pulled back into a braid. She's wearing pink sleeves. She's the only one on the screen with that color, so you can't miss it. (Slow motion can be helpful but is unnecessary).
Continuity mistake: When the Uruk-hai stop to rest by Fangorn Forest, they drop Merry and Pippin right next to each other, yet Pippin then has to crawl some distance towards Merry so that he can speak to him. [On the Extended DVD, Peter Jackson says that parts of this scene were shot two years apart, and that in fact it was made up of shots for two distinct scenes. Either of these might explain this discontinuity in positioning.]
Revealing mistake: When the riders break out of Helm's Deep, you can see the hooves on some of the horses pass straight through the Uruk-hai corpses on the bridge.
Revealing mistake: Shadowfax, the horse that only Gandalf is supposed to be able to ride, will not take a saddle and bridle, so throughout the majority of the film, they try very hard to hide the saddle that Gandalf is obviously sitting on, even though you can see him holding the front of it underneath his robes, and sometimes, you can see him holding a very thin bridle. But right at the end of the film, when you have the shot of Gandalf, Aragorn, Legolas, Gimli, etc. on horseback, you see Gandalf's feet in stirrups.
Continuity mistake: As Faramir holds the Horn of Gondor, the rope is attached to metal loops on the smaller half of the horn - without the mouthpiece. However, in FotR, when Boromir is hit with the third arrow and the Horn of Gondor is cloven in two, the rope is attached to the metal loops on the half with the long mouthpiece. (There are only two metal loops and they are permanently affixed.)
Revealing mistake: When the women and children are evacuated to the Glittering Caves under/behind Helm's Deep, in the first shot, a hooded person leans on a stalactite making it sway back and forth.
Continuity mistake: When Theoden is spouting his poem about the horse and the rider, Gamling is putting the armour on his King but when the camera returns to a wide shot, he still only has his breast plate on.
Continuity mistake: When Aragorn, Gimli, Legolas and Gandalf are galloping towards Edoras, then stop and when they are riding up towards the entryway at the bottom of the hill, Shadowfax has a white rope around his neck. However, as they're riding through Edoras, passing the people, Shadowfax no longer has the white rope around his neck.
Continuity mistake: When Merry and Pippin first enter Saruman's storeroom, in the close-up, Merry is holding an apple and a large glass carafe with wine. As the camera pans out, to show the whole storeroom, he is no longer holding the large glass carafe, but he is holding an apple and a turkey. Extended DVD.
Revealing mistake: Frodo, Sam, Faramir and Gollum are at the sewer in Osgiliath when Faramir asks, "Cirith Ungol?" and then grabs Gollum's neck. Frodo and Sam watch as Gollum is grabbed, but their eyes do not follow Gollum as Faramir grabs him, their eyes remain focused on the ground to their left. The shot of Faramir and the shot of Frodo and Sam were edited together, with Gollum added later.
Continuity mistake: When Merry is running away from the Orc in Fangorn Forest he has a big gash on the left side of his head, yet when he's in Treebeard's hands it has changed to his right side. Due to shot/scene flipping, this occurs numerous times.
Revealing mistake: Right at the beginning when Frodo and Sam are climbing up a hill, look at Frodo's left foot: One time he makes a step and his Hobbit-foot vibrates when it touches the ground. Both his feet vibrate as he walks, when he has his cloak wrapped around him.
Revealing mistake: At the Battle of Helm's Deep, just after Aragorn slices the leg off the Uruk and just before Gimli slides down between the legs of another Uruk and smashes his axe into his chest, look carefully at the Elf on the left side of the screen. He arches his bow and fires, followed by a specific shooting bow sound effect, but there is no arrow.
Continuity mistake: During Frodo and Sam's final scene in Osgiliath, you can clearly see that the chain Frodo is wearing has gotten much longer. In several shots while Frodo is on the ground, the chain hangs down below the shot, so you cannot see the Ring.