Yes, but Sifo Dyas isn't the only thing that doesn't make any sense. Dooku's discussion with Obi Wan about Jango and the Sith seems completely out of place. While I understand he is trying to trick Obi Wan, it certainly just seems like he is tired and out of the loop. Then, when he beats down both Obi Wan and Anakin, he looks upset about what he has done...but there is no way that he could be confused about right and wrong as Anakin was. Dooku seems dismayed a Sith is in power, but does everything every step of the way to help him.

He's not conflicted, it just seems like half of it was shot during production and half of it was shot during pickups and then it was all blended together.