I think I see what's happening with it, and yeah, sounds like you're right. The game thinks the feat you'd normally get on 6th level is used up for Weapon of Choice, and because Weapon of Choice isn't actually meant to take up a feat, you only have the limited list to chose to take your actual feat in.
I'd imagine you could fix it by taking your level of Weapon Master at level 7 instead, but you might not want to.