Other mistake: The battle droids - including the commando droids featured here - habitually have two broad fingers and a thumb. So how can a commando droid squeeze itself completely into clone trooper armor without its broad fingers tearing open the gloves, since it can't separate its fingers?
Deliberate mistake: At the beginning, Asajj Ventress is wearing an outfit with a long skirt. When she is rescued from her damaged starfighter by the scavengers, the skirt has vanished. This was done because the animators found the skirt too difficult to animate. This is also why she receives a brand new outfit that never had a long skirt later in the episode.
Plot hole: When Lawquane spots the droids in the field, he identifies them instantly as commando droids. But as he had left the Republic Army shortly after the first battle on Geonosis (the one which started the war) and has lived as a farmer ever since, and since the commando droids are relatively new (see "Rookies"), how can he know what they are? With his lack of battlefield experience, he should simply call them battle droids.
Question: Has Dooku ever officially made Asajj his apprentice? I know he is still Sidious' apprentice, but Sidious secretly trained Maul before he killed Plageous (according to the SW Wikipedia), so Dooku could secretly train Asajj. In "Ambush" he calls Asajj his apprentice when talking to the king of Toydaria, but then in "Cloak of Darkness", he tells Asajj that she has to prove she is worthy.
Question: When Palpatine sees the hologram of the pirate leader with Dooku, he says that a hologram can be faked, but then he believes the pirate when he sees Dooku's lightsaber. If he thinks that the pirate could have faked the hologram of Dooku, wouldn't it also be reasonable to accuse him of faking the hologram of the lightsaber?