Continuity mistake: After Shelob retreats into her lair, Sam runs over to Frodo and begins to remove the webbing. In the first front shot we see Shelob's green blood on his hands. In the next shot from the side, the amount and shape of the blood on Sam's hands has changed. Then back to another front shot and the stains are the same as in the first shot.
Continuity mistake: Gandalf discusses Pippin's contact with Sauron to the others, in the Golden Hall of Edoras. Right after Gandalf's line, "They will be," in the shot of Gandalf's back, all of his hair is in underneath and in front of his cloak, but when Gandalf approaches Aragorn to say, "You must come to Minas Tirith..." his hair is over the top of his cloak.
Continuity mistake: During Aragorn's speech to his army at the black gates, the direction the flags on the spears blow constantly changes. When we see him from behindfacing them, they blow to his right, and when we see him in the POV from within the crowd, they are blowing to his left.
Continuity mistake: After the great battle in Pelennor fields when Pippin finds Merry under the Orc, Merry says, "I knew you'd find me," and you can see that Pippin has his hand under Merry's neck/head propping it up. Then, the shot pulls back to show both hobbits, and Merry says, "Are you going to leave me?" and now Pippin no longer has his hand under Merry's neck; he is sort of stroking his hair.
Continuity mistake: The braids over Legolas' ears on his scalp, change in position, shape, and how it is braided, in consecutive scenes or shots, as well as the amount of his side hair that is swept up into the back braid. Some examples are, as he and Gimli ride Arod on the Paths of the Dead, Legolas says, "...and Isildur cursed them," and then after Aragorn says, "I do not fear death," before he runs into the Dimholt Gate. Also later in two consecutive shots, when Legolas says, "And what about a friend," and then when they battle at the Black Gate.
Continuity mistake: Faramir and his men ride out of Osgiliath, and in the first wide shot their shadows are behind them. Thereafter as they ride, sometimes the shadow is directly below them, in front of them or to their left, and as Gandalf rides towards them, in one shot his shadow is in front of him to his left. Obviously filmed at different times of the day.
Continuity mistake: When Frodo is in Shelob's lair, before actually seeing her, there is a semi close-up of a bird swinging about upside-down in the webs. There is thick webbing that stretches from the bird's body to the tip of its beak, but in the next close-up the webbing only reaches halfway down its beak.
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Continuity mistake: At Cirith Ungol, in the close-up of Frodo's face as Sam says, "I can carry it for a while," Frodo has prominent black smudges under his eyes, on his cheeks and nose. In the preceding and following close-up shots of Frodo, the smudges on his face are not nearly as dark.
Continuity mistake: When Pippin approaches sleeping Gandalf there is a shot of Gandalf hugging the cloth covered Palantir, yet when Pippin waves his hand in front of Gandalf's eyes the cloth is wrapped around the Palantir differently. When Pip places it on the blankets and opens the grey cloth, in the first close-up, then a wide shot and subsequent close-ups, the cloth lying around the palantir is arranged differently.
Continuity mistake: When Aragorn, Legolas, Gandalf, Gimli etc, ride up to the gates of Mordor, the main characters go up to the gate on their own to demand it opens. The trails the horses leave on the way towards the gate are different to those that you see in the shot when they retreat after the gate has opened.
Continuity mistake: When King Theoden is lying under his horse, when Eowyn starts to battle the Witch King, he has spots of mud on his right cheek that are very clear. After Eowyn has slain the Witch King the spots on Theoden's face are now faint smudges. After he dies and she leans down to hug him, the spots are now as they appeared in the first shot.