Maybe Padme knew where Dooku's ship was kept when she was put on trial with Anakin. Or maybe Anakin told her through the force. Or maybe the hanger can be seen off at a distance. Or maybe there is only one major hanger on Geonosis. There are a thousand possibilties. The only other plot hole I see for the most part is the Jedi ghost thing, why some disappear and some don't. Besides that, most are pretty small unless I am missing something.