This has happened three times tonight on my account (8:40pm EST) where it showed me 8800 for a flawless ruby and the pop-up to confirm showed buyout of 8800. When I go to the completed tab, the item shows as a buyout of 10000 and sure enough it took 10000 out of my gold. I'm only bought one at a time, so this isn't an issue with multiple items.
This has cost me a lot of money and Blizzard needs to get this fixed. Blizzard support said that I had to post my bug in this form.
The question from me though is, how do I get my gold back? I won't do any more gem purchasing until Blizzard gets this fixed.