Penny -
Did you see him scan your card. If you think you remember seeing him do it, then maybe it was an internal error. And, common, maybe why the manager was so frustrated, just not wanting to deal with another instance. (Of course, it doesn't excuse his behavior, either way.)
Of course, this is just to make you feel better so you don't feel so betrayed and ripped off - its a terrible feeling. I'm sorry for you that this had to happen. Please let us know how this turns out.