Continuity mistake: When the two factions of Hondo's pirates are fighting each other, the ones who sided with Maul and Savage are using blasters that fire red bolts, while the ones that stuck with Hondo shoot blue bolts. When Hondo persuades the traitors to work for him again and they attack the two Sith, all of the pirates' blasters are now firing blue bolts. This is Star Wars, not G.I. Joe, and weapons don't just change colour like that.
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. (00:08:20)
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?