I'm getting some discrepancies between my stored soul gems vs. my character's inventory. For example, petty soul gems listed as filled in the end table in Breezehome become empty after being transferred to my character. I just did a transfer of lessor soul gems: 5 were listed as common soul gem (common) in the end table. However, when transferred to my inventory only one was listed as filled and the remaining 4 empty. They were clearly differentiated between filled and empty in the end table. What could be causing this?

dropping soul gems will clear them of souls, aparently stashing them away may do this too but its much more rare.

Really? that can be kinda useful if a grand soul gets filled with something crappy.

Unfortunately, mine were all filled with the proper souls. Oh well, just gives me a chance to hunt some more wildlife.