Factual error: During the Battle of Teth (the pillared jungle planet), the AT-TE's shoot the ledge at the top and there's not a single mark in the ledge afterward despite being hit with several joules worth of fire.
Continuity mistake: When Asajj Ventress starts to make the clone trooper move up the wall (before asking where Anakin is), her eyes are green as she raises her fist at him. When she uses the mind trick and tells him to contact Anakin, her eyes are blue.
Continuity mistake: When R2-D2 closes the door to the platform in the back of the monastery (before Asajj attacks Ahsoka), Asajj stabs both of her lightsabers through the door, a few inches apart from each other, and starts moving them downward. In the next shot, on the other side of the door, there is already a solid line (the top of the circle) cut into the door. There wasn't enough time for her to have stopped and connected the space between the two holes.
Continuity mistake: When Asajj is reporting to Dooku and she tells him to wait (before Obi-wan shows up), you can see in the hologram that she ignites both of her lightsabers and turns around. However, in the next scene (at her location), there is no sign of a hologram transmitter/projector, which she would have been using to talk to Dooku. There is just a door and some battle droids in front of her. Even if she was using the handheld device that is shown earlier in the movie, there wasn't enough time for her to have put it away and gotten her lightsabers out, since Dooku's point of view shows her already turning toward Obi-wan.
Revealing mistake: When Anakin, Ahsoka, and the clones begin their ascent to the monastery on planet Teth, the "ascension cable" of one clone trooper (second from the front when the shot begins) is not animated correctly and a gap can be seen between the end of the cable and the clone's blaster.
Continuity mistake: When Asajj and Obi-wan start fighting, she throws her skirt at him and he cuts it with his lightsaber. During the rest of the fight, there are a few shots that show more of the floor or the entire floor area, but the pieces of the skirt have disappeared.
Factual error: During the Battle of Teth, a walker fires at one of the pillars. In the next shot, it hits the very top ledge. Problem is it was actually aiming at the middle, as was the other walker.