Near the end of the movie, Count Dooku uses the force to pull the ceiling down on Yoda. When Yoda uses the force to stop the rocks and push them away, a very large piece of rock smashes against the wall without making a sound.
In the arena scene when the monsters are approaching, Obi-Wan tells Anakin to "Concentrate". His lips are actually saying the original line, which was "You take the one on the left, I'll take the one on the right". This line was present in the media screenings but changed for the theatrical release.
Dooku's lightsaber has two different sound effects when he turns it on. The first time, when he is about to duel Obi-Wan, the sound is similar to Luke Skywalker's lightsaber from Star Wars: Episode VI - Return of the Jedi (1983). The second time Dooku turns his lightsaber on, when he is about to fight Yoda, the sound is the same as Darth Vader's from the original trilogy (as well as Darth Maul's from Star Wars: Episode I - The Phantom Menace (1999)).
When a Clone Trooper finds Padme after she has fallen out of the gunship on Geonosis, she tells him to get a transport ready so they can follow Anakin and Obi-Wan to Dooku's hangar. There's no way she could have know they were going there; she was unconscious when they did.
In the battle arena scene where C3PO's head is being dragged by R2D2, C3PO is heard talking. ON Bespin, C3PO's voice controls were on his back and he was unable to talk until he was joined with his body as this is where power was derived.
On clone ship following Count Dooku, Obi-wan wants to fire at Count Dooku's speeder but the ship's command reports that the ship is out of rockets. However when camera cuts to Obi-wan with wing in background 4 rockets are under the wing
When Obi-Wan is climbing out of his starfighter on Geonosis we see R4's head (dome) facing the front of the ship and then rotate left. The next cut, R4's head (dome) is facing forward again, and repeats the motion rotating left a second time.
In all the "Arrival to Geonosis" scenes, the planet is surrounded by nothing but the asteroid field. When Count Dooku retreats from the world, several Trade Federation Droid Control Ships have mysteriously appeared as well.
When Obi-Wan talks to Yoda about who might have erased Kamino from the Jedi Archives, Yoda is instructing Younglings in sabre technique. In one shot an alien Youngling appears in the back of the class, in the next, he's in front of the class. When the shot re-establishes, the alien is once again in the back of the class.
While in the arena on Geonosis, when Mace Windu is fighting the droids, his under tunic of his Jedi Garb is overlaying to his right. Shortly after, just after beheading Jango Fett, the tunic is overlaying to his left.
As clone ships fly away from the arena, the last ship loads its missiles. When it is reloading you can clearly see droids on the field. In the next shot with R2D2 and C3PO there are no droids on the field.
When Obi Wan sends the message for help to Anakin and Amidala, Amidala presses a red button in order to transmit the message to the Jedi council. A minute later she presses the same red button in order to view a map of a galaxy, without first doing anything which might be expected to change the function of the button. There have been some desperate attempts to explain this one away, but we don't buy it.
When Obi-Wan Kenobi grabs the provoking stick from the Geonosian and holds it to fend off the acklay, he holds it in the middle. In one shot, however, the stick is then shown being held towards the tip.
When Obi-Wan is at the Jedi Temple library and the elderly librarian is helping him to locate the Kamino system on the display screen, he states that it should be at the part of the galaxy's picture he points to (somewhere to the center left of the screen) but when the screen zooms in to the location, it doesn't zoom in to the location Obi-Wan points to, and instead zooms in to the center of the galaxy at the dead center of the image.
During the arena battle, two creatures of fairly significant size (the reek and the acklay) are quite clearly killed. However, during later wide shots of the arena, neither creature's corpse is visible. The reek later reappears when Boba Fett is examining Jango's severed head.
When Obi-Wan is having a drink at the Outlander Club bar, there is a woman with short blond hair sitting at his left. As he spins around swinging his lightsaber at Zam Wesell, the woman's chair is empty (he would have hit her if she was still sitting there). In the next close-up of Obi-Wan, the woman has returned to her seat (at the far left of the screen).
When Zam Wesell runs into the Outlander Club, the area beside the entrance is empty. A moment later, As Anakin and Obi-Wan arrive, there are several canisters and cases placed outside the arches of the Outlander on the right.
Padme's decoy, Corde, is seen killed in the beginning when the ship explodes, but in later scenes, we see a decoy that appears to be Corde. This is not a goof, though, as the decoy we are seeing is actually a different decoy, named Dorme (remember, since Padme's decoys obviously need to be able to impersonate her, they are naturally all going to look similar!), whom we hear her refer to by name (confirming that she IS, in fact, not Corde but a different decoy) just before she and Anakin board the freighter bound for Naboo.
During the light-saber battle with Anakin, Obi-Wan, and Dooku, Obi-wan is slashed by Dooku and falls to the floor. Dooku raises his saber to kill him. Anakin dives in and blocks his saber. In the wide shot, not only is Obi-Wan not anywhere to be seen, he almost immediately, THROWS his saber to Anakin. Neither Dooku or Anakin had moved yet. Obi-Wan should have been able to just hand his saber up to Anakin.
When Anakin and Padme arrive on Geonosis they enter the underground factories. A steel door opens above them and Padme ducks to enter. However when Anakin follows he does not duck enough and his head passes through the digitally created metal door.
When Obi-Wan is talking to Jango and Boba in their "apartment", Obi-Wan pauses. He's not moving and you can see the back of his head. When Jango walks behind Obi-Wan on the screen, you can see Jango's "shadow" through Obi-Wan.
Obi-Wan's beard is noticeably fake in several scenes. This is because actor Ewan McGregor had shaved off his beard after principal photography, and the shooting of additional scenes required a wig and fake beard to re-create his look. Shots include the scene in the elevator to Padmé's apartment, the exchange about the 'changeling' in the Outlander Club and his entire interrogation by Count Dooku.
During the tour of the Kaminoan cloning facility, there are several shots that appear to have been flipped. The giveaway is that Obi-Wan kimono overlays on the left instead of the right, and his lightsaber hilt is hanging from the left instead of the right.