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?
Other mistake: In one shot after the droid fight in Gha Nachkt's ship, at one point when you see R3-S6 (Goldie), his eye is reversed. (00:12:42)
Other mistake: When Cad Bane orders one of the commando droids disguised as a Senate Commando to finish clearing the platform, the neck area below the helmet shows human skin even though there's now a droid inside the armour. (00:02:07)
Answer: Dooku never accepted Ventress as his apprentice, as far as I know; he just kept her as his devoted personal assassin. In Phantom Menace, it is stated that there can be only two Sith at a time, to prevent a power struggle in the lower ranks. To accept Ventress as an apprentice, Dooku would have violated that rule.