I found a spell prepare glitch. It will let you unprepare a spell but not re-prepare. It happened when I equiped the Rain Maker staff which is supposed to give you the create/destroy water spell. I already knew the spell but did not have it prepared. While having rainmaker equipped It didn't add create/destroy water to my hotbar so I checked my skills and saw that I couldn't prepare spells even though I wasn't in combat. Unequipping Rain Maker fixes the issue.