Revealing mistake: In the two scenes, when Frodo and Sam are both up on the rocks and later, down below, hiding out of view, the Black Gate is in front of them. Earlier, is the view inside the gate. The two Trolls are pulling and pushing the wood 'pulley', to open the gate, while walking on the tall ramp that curves around. When the gate is open, that ramp should be in full view, from the angle that Frodo and Sam are positioned, but it is not.
Continuity mistake: When Aragorn first arrives in Helm's Deep and is confronted by Legolas, there are three close-up shots of Legolas saying, "Le abdollen" (you're late), "You look terrible," and then smiling. The bow visible behind his right shoulder appears to be his old Mirkwood bow. It is dark golden-brown, smooth, with a black bowstring. The one Galadriel gave him is the same color as his hair, elaborately carved, and has a light-colored bowstring. (for comparison check 1:43:20, where they are in the armory, and the bow should look even darker... but the white bowstring's visible there.) Continuity is screwed up as well, because in the shots between the close-ups of this conversation, where both Aragorn and Legolas are shown, the oddly-carved ends of his Lorien-bow are visible.
Continuity mistake: When Faramir and his men are looking at the map of Middle-Earth in Henneth Annûn, Minas Morgul is not shown anywhere on map. It should be at the end of the road leading east out of Osgiliath. This leads us to believe there's an non-fortified road leading straight into Mordor.
Continuity mistake: Throughout the movie, the size of Gimli changes several times. Upon entering Edoras, his height is just under Legolas' shoulder. When the Uruk-hai attack Helm's Deep and they are waiting atop the wall, you can hardly see Gimli's helmet, but all of the other characters (for example Legolas) stand there behind the wall that reaches the height of their kidney-area.
Continuity mistake: After Aragorn says to Haleth, "Give me your sword," in the wide shot we see that Aragorn is sitting on the tail of his coat and the coat is draped down the steps under his legs. When Aragorn rises, just after Haleth says, "...They say that it is hopeless," we see that the coat is not draped down the steps under his legs, as in the earlier shot. It is not the legs' shadow.
Deliberate mistake: At Helm's Deep, Theoden says, "I want every man and strong lad..." behind them is Gimli, who has a conspicuously reddish face, and his beard is split down the middle into two braids. Éowyn confronts Aragorn, she apologizes and hurries off, walking between Legolas and Gimli, who looks the same as in the earlier shot. It's obviously Brett (scale double) in both shots, the beard with its two thin braids are completely different when next we see Gimli, in a close-up at the armory. This time the beard is full, with hair between the two very thick braids, and his face is a normal color.
Continuity mistake: At night at the Dead Marshes when Frodo is lying down he is holding the Ring in his hand and he's stroking the Ring with his middle finger. In the very next close-up he's stroking the Ring with his index finger then in the next wide shot he's stroking the Ring with his middle finger again.
Revealing mistake: The very first shot of the Uruk-hai running through the rock canyon is the exact same shot that is shown in the last shot of this scene, just after Pippin bites the Lorien brooch off his cloak. Even though in between those two shots, all the Uruk-hai have been running until they meet up with the Orcs. In between those two shots, the rock formation shown behind the Uruk who lifts his fist up is also quite different in the next successive shot, when the Orcs approach the Uruks.
Continuity mistake: Faramir captures Sam and Frodo. Faramir goes over to the dead body, and says, "His sense of duty was no less than yours, I deem," and rolls over one of the Haradrim with his foot. The dead man is lying with his face towards the ground. In the earlier shot, when he fell off the Mûmak and landed behind Frodo and Sam, the right side of his face is lying on the ground. It is the same man in both shots.
Continuity mistake: When Sam first reaches into his pack, in the close-up, he takes out the lembas bread and says, "Oh yes. Lovely", one corner of the leaf is sticking up. As he continues to say, "Lembas bread", in this wide shot, all the corners of the leaf are now down and completely covering the lembas bread.
Continuity mistake: Elves, as can be seen all through the battle of Helm's Deep, carry their sword and arrows on their backs, protruding some distance above their shoulders. When the elves arrive at Helm's Deep, however - none of them appear to be carrying a sword (it is possible that the sword could be sheathed at the waist, under their robes, but it seems unlikely that they'd change it to a back-sheath later on), nor do they have any arrows for the bows that they are carrying.
Continuity mistake: At Helm's Deep, in this opening wide shot, soldiers call out, "Come on, keep moving. Quickly now," as the people walk towards the Glittering Caves. We see the soldiers standing up against the wall, as the people go past. Next, in a side close-up, Aragorn talks with Legolas as they walk past the soldiers, and other people. In the next shot from the front, as the conversation continues, they're still walking past the guards and people. In the second and third shots the people around them differ and in all three shots the guards differ too.
Continuity mistake: The first two shots of people leaving Edoras are shown, and in the wide shot Éothain and Freda are seen on their horse, as well as the people in front and in back of them. Next are shots of Theoden and Gamling speaking, and the Aragorn and Éowyn confrontation. Then in the next shots the people are still seen leaving Edoras, including Éothain and Freda with the same people in front and in back of them as was seen in the much earlier shot!
Deliberate mistake: Legolas leaps onto Arod and as he rides, both of his hands are clean. After they've just clashed into the Warg riders, in the close-up of Legolas as he releases his arrow there are dark smudges visible on Legolas' fingers and knuckles on his right hand. In the close-up of Legolas as he lets loose the arrow into the Warg that is about to attack Gimli, we see both of his hands are smudge free. This shot is flipped, so the right hand that was previously smudged is now the left hand, which is clean anyway.
Continuity mistake: Before Gandalf makes his reappearance, when Gimli says "The air is so close in here" he has two axes at his waist, one in hand (and one on his back as seen earlier). The axe on his waist at his left has a solid head. Later, when Aragorn tells him to lower his axe, one is missing from his waist. It reappears in his hand just as Aragorn starts to draw his sword. Then, just as the three are about to attack the wizard, Gimli doesn't appear to have an axe in his left hand. Yet, in the subsequent cut, he throws one with his left hand. Then, when Gandalf reveals himself and Gimli bows his head, the solid-bladed axe appears to have moved to the right-hand side of Gimli's waist (as they cower in Gandalf's brightness).
Continuity mistake: Merry and Pippin run into Fangorn Forest and drop down on the ground. First there is a wide shot of Pippin falling, then there's a close-up of them, and last there's an extreme wide shot of the area. The area that Merry and Pippin are lying in is different in all three shots.
Continuity mistake: After riding down the Causeway at Helm's Deep, Aragorn looks up and sees Gandalf. In the first shot his hair and face are very sweaty and shiny. In the second shot when he says, "Gandalf," his face is dry and sweat free. His hair is different in both shots too. The second shot was pinched from the earlier scene in the Keep when he looks up at the window remembering Gandalf's words, "Look to my coming." Confirmed on commentary.