"I didn't recognize what i found as a rune. " probably the case, they look like gems(since I didn't finish doing graphics for all of them) and there's an unlabeled count for how many of them you have and how many are in the room total,

For why you can't do certain things I'm assuming you're mainly talking about not being able to use Leap despite it not being grey(or not knowing why it is grey) and possibly the first number next to a spell indicating it's rune/gem cost might not be as clear as it could be.