I contacted support and it seems to be a bug, they said "I strongly encourage you to directly submit an in-game bug report as well by opening the Game Menu and select Help". If other people have this problem and they do this enough times, hopefully they will take care of it come next patch.
I got 3 of each rune and refined the item i was supposed to, the problem is after that. I have the red stone but I cant buy anything with it at her store