I noticed the same with a few runes. I realized it was because it’s counting both the runes on your sPvP gear and the ones in your PvE gear everywhere, in- and outside sPvP, so if you have six divinty runes on both gearsets, it’ll show 12/6. Tested it by changing around my sPvP runes inside the mists, then going back to Lion’s Arch to see if my stats had changed, which they had.
I don’t know if it actually affects my damage in combat, but the character sheet is definitely counting runes on both gearsets.