Oh, yeah, you´re right! Anakin has much too much encounters with Dooku IMO, isn't it. In the movies it looks rather like that he had his first encounter in "AotC" and than just the second one in "RotS". You never had the feeling that they maybe met more than once before. But well, lets better look at it as if it plays in a parallel story and dont worry about if it fits with the real movies. Because all in all its justa cartoon series.