After Legolas shoots two arrows into the shoulder region of the Uruk-Hai running with the torch, the arrows are nowhere to be seen in the shot that shows the runner diving into drain on the side of the wall of Helms Deep.
When the Rohirrim surround Aragorn, Legolas and Gimli at the beginning, you can see Éomer's lips moving in one of the wider shots and he obviously talks to the three but there is no sound coming out of his mouth.
During the battle of Helm's Deep, Aragorn orders the archers to shoot by yelling 'Fire!'. This command appeared after the introduction of firearms. Earlier, an archer commander would use the command 'Shoot!' or 'Release!'.
Legolas' eyes are brown for the majority of the battle of Helm's Deep, instead of their customary blue. However, it is reported that this particular color change came about when Orlando Bloom's blue contact lenses were forgotten during some of the shooting for this sequence.
When Gandalf the White first enters Theoden's hall, the position of his staff changes from being held perpendicular to the ground to being held parallel between shots. Director Peter Jackson noticed this error for the first time while recording the Director's Commentary for the Extended Edition of the DVD.
Pippin's hands are tied, but when he falls under the horse, his hands are untied and apart. When Aragorn is working out what happened we see, in the flashbacks, that Pippin did not cut his bonds until after the horse incident.
While on their way to Helm's Deep, Gimli is telling tales to Eowin and Aragorn in order to while away the long hours of the trip. At several points, however, you can see the direction of the battle ax's head change from blade forward to blade backwards then forwards again, all within mere seconds of each other.
When King Theoden is having his armor strapped on, his aide fastens the left shoulder strap, then we see the leg greaves being strapped on, and gloves being tied. In the next shot, the aide goes to fasten the left shoulder strap again, and there are no greaves on his legs or gloves on his hands.
When Frodo and Sam are hidden under the elvish cloak at the Black Gate, we can see from under the cape the feet of the enemy soldier through a gap in between the cloth and the floor. But in the next shoot when Frodo unfold the cape (that looks like a rock) we can see it was well buried in the dust and there is no possible gap.
While everyone was amazed by Legolas' skill in firing three arrows in quick succession whilst sliding down the stairs on an Uruk-shield, you can clearly see that each shot is cut when he is about half way down the stairs, i.e. he only had time to fire one arrow.
When Frodo, Sam, and Gollum are in the Dead Marsh and the Nazgul flies over, Frodo goes after the ring with his left hand, which Sam grabs and holds. Frodo is then shown putting his right hand to his chest, but in the wide shot, his right hand is still lying at his side.
In the storeroom where Sam is suggesting that Frodo use the Ring to escape, Frodo is initially sitting in front of a barrel. When Faramir arrives, Frodo and Sam are sitting on a cloak and there are no barrels in sight.
When Legolas shoots the rope of one of the big ladders, the previous shot has already shown the ladder to be past straight vertical position. The ladder should continue it's arc towards the wall, but instead it falls back.
When Aragorn, Legolas and Gimli are first introduced to Gandalf the White in Fangorn forest, Gandalf replies "yes, Gandalf, that is what they used to call me, Gandalf the Grey" when Aragron mentions his name. In reality, Gandalf would already be aware of his name as Treebeard had previously delivered the Hobbits Merry and Pippin to him, who would of obviously called him Gandalf when they met him.
When Legolas is pulling Gimli and Aragorn to safety using the rope during the battle of Helm's Deep, Gimli is on Aragorn's right side for every shot except the first close-up of Aragorn in Gimli, where he is clearly on Aragorn's left.
When Merry and Pippin are dropped to the ground by the Uruk-Hai, Merry is lying very close to Pippin. In the next shot Pippin is obviously a few feet away for he has to crawl closer to Merry to be able to talk to him
In Helms Deep, as Legolas throws the shield onto the stairs, he has his bow in his left hand. As he runs to jump onto the shield, the bow is gone. As he is sliding down the stairs, he is using the bow again.
When Gandalf and Theoden are talking outside town, near the burial mounds covered in white flowers, all the shots of Gandalf show the wind whipping his hair around, but in all the shots of Theoden there is not even a hint of a breeze in his hair.
When the three ladders are raised on the Keep in the Helms Deep sequence, the wide and close-in shots alternate between the outer two ladders being about 30 feet apart and less than 5 feet apart, respectively (the third is in between them and never makes it up).
When the orcs are carrying Merry and Pippin on their backs the wide shots show the orc carrying Pippin to be closer to the camera with the orc carrying Merry to his left. But in the close-ups they have swapped places with Pippin having to turn to his right to speak to Merry.
When Aragorn, Gimli, Legolas, and Gandalf first enter the Golden Hall of Edoras, Legolas is supporting Gandalf with his arm. When the door is shut behind them he lets go and in the next shot their arms are together again.
In the scene where Treebeard the ent is carrying Merry and Pippen through the forest explaining to them about the lack of Ent-wives, the location of the branches around his head keep moving. Either they are from the side of his head and his shoulder, two out of his head, or none at all.
When Éomer and company ambush the Uruk-hai, we see Pippin as he is almost trampled by a horse. When the shot cuts to Pippin, his arms are unbound and free as he moves to defend himself. When he rolls away, however, his hands are bound.
Very near the beginning of the Extended version, some of the real fog in a valley visible at a distance behind Frodo and Sam abruptly disappears. While some close-ups were filmed in studio, it is also possible that there was a delay in filming these "on location" shots.
At the beginning of the battle at Helm's Deep, the people in the fortress are seen drawing their arrows before one of them is accidentally released. Soon, they are seen drawing their arrows again, despite the fact that they should have still been drawn from the first time.
Near the end of the battle for Helm's Deep, Theoden, Aragorn and others are waiting for the Orcs to break through the door. In the next shot they are on horses charging toward the Orcs. There were no horses around to begin with.
While Aragorn, Legolas, and Gimli are tracking the Uruk-hai, Aragorn asks "Legolas, what do your elf eyes see?" And Legolas responds, "The Uruks turn northeast, they're taking the hobbits to Isengard!" If the Uruks turned northeast, they would be traveling away from Isengard, since Isengard is northwest of their location.
During the battle of Helm's Deep, after the wall has been breached and Haldir dies, Aragorn gets on an Uruk-Hai ladder and drops himself into the advancing Uruk-Hai. In the wide shot it can be clearly seen that the ladder has been raised against the Deeping Wall from inside the castle. When, how and why did the Uruks raise a ladder there, when two flights of stairs are already available?
When the gate to Mordor is opened, it is clearly seen to be as thick as the wall, and each corner is seen to be a right angle. There is no space at all in between the gate and the wall when it is closed, later on in the same scene. However, the gate opens on a curve, and so would get stuck every time it opened or closed, unless the wall was somehow retracted. We do not see the wall retracted at all, thus it is physically impossible for such a gate to exist.
During the battle with the Warg riders, a Warg and Orc fall across Gimli. Visibly struggling to lift them off, there is no change in effort or position when a second Warg puts its weight on Gimli. This should be an addition of several hundred pounds.
In the extended DVD edition, Dominic Monaghan points out in the cast commentary that in one of the aerial shots of the Uruk-Hai taking the Hobbits to Isengard, Merry and Pippin are nowhere to be seen. This is false. Both Hobbits are wearing green capes which can be easily made out without freeze-framing the scene. The Hobbits are being carried by two Uruks in the third line from the front of the group. (Extended Edition DVD Time Code: Disc 1, 26m20s)
When Shadowfax first appears, there are tracks across the paddock behind and to the right of him. Some say these are tire tracks, others argue that they could just as easily be the wheel ruts of a farm cart. In response, the first group say that the ruts are too far apart to be from a farm cart, and the space in between is too narrow, meaning that they are definitely those of a car or truck.
When Faramir's party is called back to Osgiliath, they stop on a ridge looking toward the city. In the distance, you can see Minas Tirith, which is west of Osgiliath; therefore the party is on the eastern side of the Anduin. Once they reach the city, one of the men of Gondor mentions that Mordor's forces have taken the eastern half of the city. So how did Faramir's party get to the western side? If they used the sewer that Faramir sends Frodo and Sam into later, why did he have to explain to them what those sewers were at that time? They'd already have been through them once.
(Flipped shot) When Legolas says in Elvish, "There's something out there," the Elvish Brooches (leaf brooches holding their cloaks together) are facing the opposite direction. Peter Jackson first noticed this error while recording the Extended DVD Director commentary.
In Helms Deep, when people are moving deeper into the caves (as orcs are storming the keep), we see a woman put her hand on one of the stalactites as she passes it. When she releases it it sways gently.
This was changed on the DVD, but on the original version of the movie, during the battle of Helms Deep the orks launched ropes with hooks on them at the top of the wall. They started to hoist the big ladders with the ropes. Two scenes later they pushed the ladders the rest of the way to the wall but the ropes were not there.
When Theodred is carried to the graveyard, his heavy scale mail armor is caught in the wind; a heavy looking item supposedly made from steel plates with tough leather on the backside, but none the less it flaps in the wind.
(flipped shot) When Aragorn is tracking Merry and Pippin from the orc pyre to Fangorn Forest, his ring (usually on his left hand) is on his right forefinger and his glove (usually on his right) is on his left hand.
When the Rohirrim are searching for the body of Théodred at the fords of Isen, Éomer rolls over the body of a Rohan soldier. Next to him you can clearly see a piece of yellow and black striped tape (in the bottom left corner), possibly a marker.
When Gimli kills the warg just after the battle on the mountainside, after Aragorn goes over the cliff, there are riders in the background acting out killing moves against the enemy. However there are no enemy present.
When Gandalf is riding Shadowfax "bareback", there is clearly a saddle under his robes and his feet are obviously in stirrups. In some frames it appears to be a Western saddle, because as the robes flap around it, Gandalf and/or his stunt double appear to hold the horn.
The goof items below may give away important plot points.
When Gimli enters Helm's Deep for the first time, he speaks to Eowyn about Aragorn's fate. Before she speaks, Gimli's helmet is on and his axe is covered in blood. After she speaks, his helmet is off and his axe is clean.
Near the end of the film, when Frodo and Sam are in Osgiliath, the chain around Frodo's neck with the ring on repeatedly switches between being caught around one of his buttons and hanging freely between shots.
When Gamling and Hama ride ahead of the Rohan civilians to scout, and Hama's horse starts to get nervous and Gamling asks what's wrong, Hama is on the right and Gamling is on the left. Then in the next shot they switch places. And when the Warg jumps upon Hama they switch places again.
As Théoden, Aragorn and the others ride out of Helm's Deep at the end of the battle, when they ride down the "bridge", one of the computer generated Orcs, on the side of the bridge that is closest to the camera, goes straight through one of the horses before he is thrown from the bridge. Also (and conversely), horsemen in the back of the column slash with their swords at invisible targets.
At the very end of the movie, when Gandalf, Theoden, and rest of the main survivors of Helm's Deep ride over the hill together, and Gandalf says "The battle for Helm's Deep is over. The battle for Middle-Earth is about to begin.", the actor portraying Eomer is clearly not Karl Urban. This shot was done during pickups when Urban was not available, but WETA was supposed to cover up the actor's face with Urban's.