Left click on the crystal bag to open its window, if necessary move it so that window is not overlapping the inventory window, then drag and drop crystals from the inventory to the crystal bag window.
Before the
patch there was a bug with the act 1 level 2 dungeon where it would be empty. Other dungeons and acts should be fine, AFAIK.
After installing the patch, the BF merchants' inventories (including gold) will regenerate each time you enter.
