for some reason, right after opening the trade dialogue with the Riddler in act 3, the 2nd floor of the dungeon where you are to retrieve a book for Cytha and/or the amulet for Zandalor, and then closing it to access inventory
(and i have no idea what caused this: if this is related to the process above, or the fact that there was an issue with the gem bag disappearing that was corrected in the recent patch),
but for some reason, when i opened the bag and removed crystals, they were duplicated once each instead of removed, so i dropped one in inventory while the original remained in the bag. i was able to repeat this once for each slot in the bag before it stopped working.
helped me get something i needed from the Riddler though <img src="/ubbthreads/images/graemlins/biggrin.gif" alt="" /> without losing any nice crystals. .:heh:.
but i just thought i would let someone know.