I know the one that bugs me is how (I forget the name of the book now) we find out from EU that Sifo-Dyas was indeed the person who made the order for the clones, and Dooku found out about this and killed him off afterwards. That's just really fucking stupid because why would a Jedi go off on his own to create an army, especially after Mace's "We're not soldiers" line, and where did he get the money?
Not to mention the rather outstanding coincidence of Sifo doing this and Dooku finding out. It would have made much more sense for Dooku to kill Sifo and impersonate him to the cloners, but nooooooooo, someone had to throw in a ridiculous twist.
I've read some good EU that can cast a unique light on the events of the films, and a lot of bad EU that just really makes a mess of things. Rebuilding the Falcon without Han's approval, are you kidding me?