Continuity mistake: After Obi-Wan's group has abseiled down the wall of the prison, two of the clone troopers in armour are carrying Separatist blasters instead of the Republic-issue blasters they had before and after. (00:09:38)
Continuity mistake: Besides Obi-Wan, Even Piell and Commander Cody, the exact number of people in Obi-Wan's group keeps changing.
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.