I'm struggling with the same problem, Will, as is one of my alliance members. It cost me duplicate 18s and my ally duplicate 30s.
I've beaten ironangel up about this, and he agreed to look into it, but this is be most recent pm from him on 10/1:
OK, looking at the Medal history report, I see the loss for 18, but only one instance of it. The next transaction is 3 hours later, for -15. I need to confirm with someone how the rows are calculated, which I can do first thing tomorrow AM, to see if this is a dual ding, or what. Thanks for hanging in there!