Just before the fight scene between General Grievous and Obi-Wan, Obi-Wan uses the Force to drop a large vent-like object on top of Grievous' guards. In the fight scene that follows however, the object has disappeared.
When Obi-Wan and Anakin enter the elevator on the Trade Federation flagship, they kill several battle droids. In every other take shot in the same elevator, there are no parts left on the floor. The part of the ceiling that Anakin cuts out also disappears. Also, when the elevators stops the first time, a battle droid's hand can be seen standing in the left corner; however, when the shot changes, it disappears and then re-appears again in a shot near the end of the sequence.
When Padmé tells Anakin she is pregnant watch the pillar behind them - its design changes throughout the scene.
When Yoda uses the Force to send Darth Sidious flying across the room, Sidious lands in his desk chair which knocks over backwards. In the next shot where the desk is visible, the chair is standing back up again.
Anakin's scar on his right eye changes length and position among shots. Also, on the DVD box cover, Anakin clearly doesn't have a scar, but posters have artistic license.
During the first part of the escape from the Invisible Hand, when the decks tilt, objects (such as R2-D2, for instance) lose traction and slide "downslope". This would not happen on a ship in which an artificial gravity field was in use. "Down" would always be straight towards the deck, no matter how the ship was oriented with respect to its exterior surroundings. The sliding objects on the ship behave as if the source of gravity was outside and below it. Of course, without internal artificial gravity, everything on the orbiting ship would be in freefall.
After Anakin destroys the shield control panel in the Mustafar station, the station platform begins melting and falling apart, yet Anakin and Obi-Wan continue to their duel only a few meters above the lava river. Unless there is an unwritten plot that the Force protects its users from extreme temperatures, they should at least be suffering from intense hyperthermia, if not blistering and burning as Anakin did when he was defeated.
When the buzz droids are destroyed on Obi-Wan's fighter, they are swept away as if by wind flowing over the wings. As there is no air in space, the wreckage of the droids should have remained on Obi-Wan's fighter.
When the Chancellor announces he is converting the republic into an empire, Yoda and Obi-wan are in the Jedi Temple and discuss the empires future. This is not possible since they have no way of knowing that the empire had been created, they would have referred to it as the republic.
The button Padmé pushes to start her ship near the end of the film is the same "magic" button that has two functions in Star Wars: Episode II - Attack of the Clones (2002). It's shot in exactly the same way and is a deliberate joke.
When Bail Organa lands at the Jedi Temple, some of the clone troopers that approach him are right-handed, while others are clearly left-handed. As genetic clones, all of the Clone Troopers would be the same, either right- or left-handed. Most experts now agree that genetics aren't the only factor when it comes to handedness, and it isn't entirely implausible for some clones to have naturally grown up left-handed instead.
Just after Order 66 is given, the zipper in one of the Wookie costumes (the one on the right hand side of the screen standing behind Yoda) has been said to be visible. In fact, it is merely part of the background peeking through the Wookie's legs.
The Jedi Shaak Ti can be spotted in a hologram. However, in a deleted scene (that's available on the dvd), she is shown being killed (impaled with a lightsaber) by General Grievous during the Battle of Coruscant (which event takes place before she's seen in the hologram). This is because the scene was deleted from the final cut and is not considered 'canon' to the film's story.
When Anakin arrives on Mustafar and is shown putting on his hood, his mechanical arm is missing.
When Palpatine battles Mace Windu and his fellow Jedi Council members, Palpatine's lightsaber handle changes to Anakin's handle. This is because the scene was originally shot with Palpatine using Anakin's blade.
General Grievous, whose two arms can split into four, has a total of twelve fingers (six on each hand when his arms aren't split). However in some shots (such as when he orders his ship's bridge crew to fire the emergency booster engines in an early scene) we can clearly see he has five on each hand when his arms aren't split. In other shots, he has the correct number of fingers.
When Padmé enters her royal Naboo starship bound for Mustafar, the Coruscant skyline is full of air traffic. Yet none of the traffic is reflected in the ship's shiny mirror-like body.
Many of the computer-generated light sources do not cast light on the very real actors. For example, when General Grevious has a lightsaber in Obi-Wan Kenobi's face, and then Chewbacca (near the end) is very close to Yoda's single-person spacecraft taking off with jets firing.
After Order 66 is initiated, Obi-Wan and Yoda return to the Jedi Temple whilst Bail Organa and Padmé attend Palpatine's special session of the Senate on Coruscant. During this session, Palpatine announces his plan to reform the Republic into an Empire.
In the Temple as they are reviewing the hologram recordings, Obi-Wan and Yoda both refer to Palpatine as "the Emperor" even though it is impossible for them to know about his announcement at this point because both events are happening simultaneously.
In the Temple as they are reviewing the hologram recordings, Obi-Wan and Yoda both refer to Palpatine as "the Emperor" even though it is impossible for them to know about his announcement at this point because both events are happening simultaneously.
When Padmé is trying to convince Anakin to turn from the dark side on Mustafar, Anakin says "And I'm doing it for you, to protect you," but his mouth says "And I'm doing it because I love you, to protect you."
As Darth Vader leads the 501st Legion up the steps of the Jedi Temple you can hear their steps, marching in perfect unison, yet you can see that their steps not only do not match the audio, but they are not in sync with each other either.
On the ship, whilst discussing Anakin, Mace Windu says "I don't trust him", yet his mouth seems to say something different.
When Obi-Wan and Anakin are having their exchange of words following the landing at the Senate building, there is a strange echo when they speak to one another. Neither one is indoors, and there's nothing nearby to create an echo since they are using regular speaking voices.
At the start of the film when Palpatine is captive he says "Count Dooku" to draw the heroes attention to the villain whom has just entered the room. But Palpatine's lips are saying something else.
The Skywalker twins are separated at birth so Vader doesn't find them. Why then raise Leia in the home of one of the Empire's most outspoken enemies? Furthermore, why give Luke to his only known relatives without even bothering to change his surname?
If Mace Windu can see Anakin's conflict and fear through the Force, he should also unravel Padme's pregnancy and their relationship, just as Palpatine and Vader will later be able to see details of Luke's thoughts.
Uncle Owen, Aunt Beru and Obi-Wan Kenobi live nineteen years on Tatooine between this movie and A New Hope, but seem to have aged twice as much. If this is some feature or side-effect of the planet, then Luke should also look like he is in his late thirties when he appears next time.
"Only a Sith deals in absolutes" is an absolute.
Yoda tells Obi Wan that he is not powerful enough to take on Palpatine. It never occurs to either of them that they could both attack Palpatine, then worry about Vader later.
Obi-Wan declares an end to his duel with Anakin, and himself the winner, by stating that he has the high ground. Both he and Anakin/Vader have managed to turn the tide of a duel despite being on the low ground. Darth Maul had the high ground on Obi-Wan by pushing him into the reactor core, but Obi-Wan managed to use the Force to pull himself out of it. Luke Skywalker had the high ground over Vader while on the catwalk in the throne room of the Death Star, but Vader managed to cut him down.
Captain Raymus Antilles looks nothing like he did in Star Wars: Episode IV - A New Hope (1977), he also looks like a young man in that film, when he should be about 20 years older.
During the battle among Anakin, Obi-Wan, and Count Dooku, Dooku kicks Anakin away while levitating a defenseless Obi-Wan. He should have seized this opportunity to easily kill Obi-Wan instead of simply Force-throwing him across the room.