Continuity mistake: On Utapau, when Obi-Wan faces off with Grievous, Grievous sends 4 magna guards at Obi-Wan. Obi-Wan force-pulls something from the ceiling to crush the droids. But in the ensuing fight between Obi-Wan and Grievous afterward, the ceiling thing and crushed droids are gone.
Continuity mistake: In the scene where Anakin arrives on Mustafar and tells R2-D2 to stay with the ship, he pulls the hood of his robe over his head with two organic hands. His right hand should be mechanical. [This mistake is mentioned in the audio commentary: this shot is taken from a shot of Obi-Wan later in the film when leaving Padme's apartment. Still a mistake, though.]
Continuity mistake: When Obi-Wan meets Anakin on the landing bay of the volcanic planet, Obi-Wan comes down the ramp from the ship and removes his cloak. It lays across the end of the ramp. The shot changes, then comes back, and the cloak is now bunched off to one side.
Continuity mistake: During the Anakin/Obi-Wan fight scene Obi Wan switches lightsabers with Anakin. When Anakin is strangling him we can definitely see that Obi-Wan is holding Anakin's lightsaber in his right hand (note the hilt design), but when the shot is reversed Obi-Wan is holding his own lightsaber in that hand.
Revealing mistake: When Yoda knocks Darth Sidious backwards over his chair, you can see the stuntman's hand. Sidious's hands are old and his nails are dark around the cuticles, but the hand during the flip is perfectly healthy and a different size.
Continuity mistake: When Palpatine fights the four Jedi Masters, his lightsaber hilt changes from his to Anakin's and back again. This happens throughout the scene. [This mistake is pointed out in the text commentary.]
Continuity mistake: When Anakin is in the medical centre lying on his back being transformed into Darth Vader, you can see the main part of the mask being lowered into place but Anakin is not wearing the neck section of the mask that it connects to. We then see the main part lowering directly downwards, in the next shot the neck section is in place.
Other mistake: During the opening space battle, Obi-Wan's ship falls under attack by buzz-droids, who proceed to cut into his fighter, disabling a number of systems and leading Anakin to try some decidedly dangerous moves to get rid of them. Both Anakin and Obi-Wan are acknowledged experts in the use of the Force and both have been shown to use the Force routinely, even for relatively mundane activities. It's also been firmly established that the Force works on droids and that the Force-user can still affect others through windows, viewscreens and so forth. Yet neither thinks to use the Force to deal with the buzz-droids.
Continuity mistake: In the scene where Anakin returns to Padme's apartment after the fight at the Jedi temple, watch R2-D2 in his compartment in Anakin's ship as the camera angle changes. In some shots, R2's "legs" are flush with the hull of the ship, and in others, they are well above it.
Other mistake: To escape from the elevator, Anakin cuts a hole in the ceiling. Later, when they rescue the Chancellor, they almost get crushed by another elevator (it is another one. Each elevator has a number. Obi Wan said the number of this elevator before and it was different than the one that had the hole). However, when a shot of this elevator is shown, it has the same hole that the other elevator has (better seen in slow motion).
Continuity mistake: When Palpatine is talking to Anakin in his office, there is a table at the end of the hall with a large object in the middle, and a gold cup on each side. When they leave the office and are talking in the hall, and a thin purple lamp/object appears on the end of it for a few shots, and vanishes whenever seen from then on.
Continuity mistake: When Mace Windu and Palpatine fight, Windu backs Palpatine into the corner of the window. Note how close Windu is to Palpatine the whole time. Then from Anakin's perspective, Windu takes a few steps toward Palpatine, his saber pointed at Palpatine. When we saw it from the earlier perspective Windu never took those three steps toward a stationary Palpatine.
Continuity mistake: When the Emperor says "I have waited a long time for this moment my little green friend." Yoda can be seen laying beside his cane on the purple carpet. When they show him standing up, he and the cane are now further back toward the wall on the tan part of the carpet.
Audio problem: After the buzz droids land on Obi-Wan's starfighter, Obi-Wan says, "I'm hit. Anakin?" As he says, "Anakin?" his head is turned to the side, but you can see that the last word doesn't match his lips or the motion of his jaw.
Continuity mistake: In the scene where Plo Koon gets blasted by his Clone Troopers, the exterior shots show he is in an Episode II starfighter (closed/pointed bow, no small rear window on cockpit canopy- best seen as the Emperor gives the order), yet the interior shots of his cockpit show he is inside an Episode III starfighter (forked bow, small rear window on canopy- same as Obi-Wan's starfighter).
Continuity mistake: After Anakin has told Windu that Palpatine is the Sith Lord, Windu gets on his ship which takes off. We see the ship's shadow moving on the ground right next to Anakin. When it cuts the shadow from the ship is gone. When it cuts again to a wider shot we see the ship's shadow suddenly appear again.
Continuity mistake: When Mace Windu departs to confront Palpatine, as the ship takes off, Anakin's position on the floor differs from the previous shot, seen from the lines on the floor.
Continuity mistake: When Anakin is watching Padmé while she's brushing her hair, in the shot from behind him, his shadow on the wall differs from shadow seen in the rest of the scene.
Continuity mistake: When Obi-Wan kicks Anakin for the second time as they fight on the huge table, as the shot ends, Anakin is about to land on the right side of the table. In the next shot, he lands on the other side, and in the following shot, we see the impact of him landing again. Also, his position as he lies on the table keeps changing between shots. This is easy to see in the wide shots, and in the close-ups, where it can be seen from the pattern and the lit strip on the table. Also, notice that as his lightsabre flies into his hand, his hand is on the edge of the table, but in the previous and following shots, he was lying too far away from the edge to reach it.
Continuity mistake: Before the lightsaber battle between Grievous and Kenobi, the area where they are standing and where Kenobi "drops" the weight on the magna droids is a solid floor. The whole preparation-for-battle-scene does not include much movement from the actors. As soon as Grievous begins to move in on Kenobi, both of them are suddenly standing on some sort of bridge, without even passing the dropped weight.
Audio problem: After Anakin is appointed to the Jedi Council, Ki-Adi-Mundi says, "What about the droid attack on the Wookies?", but the first two words don't match the movement of his lips. (Even though he's an alien, his lips always move like the lips of a human.).
Continuity mistake: When Obi-Wan and Yoda walk through the Jedi Temple after order 66, in the second shot, they are standing on a round circle on the floor, but in the previous shot, they were a few metres away from it.
Continuity mistake: When R2 is at the terminal near the beginning, the two super battle droids start to walk over to him and their red dots are on the left hand side but when they get to R2 they have moved to the right hand side.
Continuity mistake: When Obi-Wan jumps to the high ground during the duel with Anakin, in the shot where he lands, his lightsabre is held parallel to the ground. In the next shot, it is pointing downwards, and in the following shot, it is pointing slightly upwards, and his left arm is positioned differently from the previous shot.
Continuity mistake: When Padmé is in her apartment and Anakin is in the Jedi Council chamber, they look out across the city toward each other. The position of the setting sun and the direction of its light across their locations is not consistent given what we are shown about their relative positions and the directions they are facing.
Other mistake: During the scene of Anakin's transformation into Darth Vader, there is a close up shot of his face just before his helmet is put in place. All of his face is shown as being badly burned with the exception of his eyelashes, which are still impossibly there. Subjecting one's face to any heat source hot enough to sear one's face will also burn away one's eyelashes as well.
Continuity mistake: During the Sidious and Yoda battle, the number of missing pods off the wall isn't consistent between shots. Sometimes a few are missing, then a lot then back to a few.
Continuity mistake: When the Emperor and Yoda flip backwards out of the pod from the "kickback" of the Force lightning the Emperor falls onto the sloped side of the pod.When they show him again he is hanging on the side of the pod with handles.(If you look at the pods each has a sloped side and a part with guardrail or handle)
Audio problem: After Anakin kills Count Dooku, Palpatine says, "Remember what you told me about your mother and the Sand People." In the next shot, his head is shown from behind, but if you watch closely, you can see that his jaw is moving as if he were talking, but nothing is heard. Use zoom for confirmation.
Continuity mistake: When the clone troopers kill Aayla Secura, the blue-skinned Jedi, their blasters are held differently between the second and third shot.
Continuity mistake: When Anakin chokes Obi-Wan, the sleeves of Obi-Wan's tunic move up and down his arms between shots, especially his right arm.
Continuity mistake: In the scene following the crash landing of Grievous's flagship where the shuttle is approaching the Senate's "parking garage" (not the Senate building itself or the Jedi Temple as others have said), the shuttle is approaching a section of the landing platform that is void of any other ships. However, in the following shot, another shuttle with different coloring and larger size is in plain view.
Deliberate mistake: In the final stages of the Obi-Wan/Anakin battle, they are fighting while floating over lava on a piece of metal. Just before Obi-Wan jumps to the high ground, we get a close-up shot of Obi-Wan (lightsaber pointing left off-screen) and then Anakin, (lightsaber pointing right off-screen) In this shot, Anakin's right hand is uncovered/real, and his left is gloved/mechanical, when it should be the opposite.
Audio problem: In the beginning of the scene in the Opera House, the audience is cheering and clapping, but in the two shots where the audience is shown, all of them are sitting still with their hands in their lap.
Continuity mistake: When Anakin is denied the rank of master and he replies "what?", we see a ship near the bottom of the window that has just passed the window frame. In the next Anakin shot, the same ship is once again just passing the window frame.
Continuity mistake: When Padmé is waiting for Anakin by the column, and also when she's talking to him, the floor around the column keeps changing between shots. For example, when Anakin runs to her, the red area around the column is much bigger than in the previous shots.