I have 5 Lesser Quen stones, 4 of them are in one stack the other by itself. When I go to a blacksmith to combine/upgrade them it says I have I'm missing ingredients 0/2 Lesser Quen Stones.
I am having the same issue. I have multiple stacks of Lessor Aard, Igni and Quen, with some stacks as high as 10-12 and then one random by itself. I am also unable to upgrade/combine them into the next level of runestones. Sounds like I am bugged also?
Patch 1.05 for consoles should be out next fix and fixes that issue. The only thing you can do on the consoles now is to sell all the "old" runes, and craft/loot/buy new ones which should work.
This particular bug, where I have 10 lesser glyphs but I can't craft normal or greater, is to me at this time the worst bug in the game. Sadly, I am not sure the patch notes shared in 1.06 will include this.