Correct, just 2 transactions for the same bitcoin. Both show up at their destination like any other bitcoin would, but only one is confirmed and the other one disappears (remains unconfirmed forever). This customer waited till he saw it in his blockchain to leave, then as he's driving away I accidentally double spended him and his coins were back in one of my wallets. I called to explain, mostly since I've never seen that before, and sent it back to him.
Due to the events of last night, I will be waiting for 1 confirmation from here on out.
I wouldn't even call what you did a classical double spend. A simple definition of a double spend is the following:
Double-spending is the result of successfully spending some money more than once.
What wallet did the customer use? If it's blockchain.info then it has something to do with them. I'd like more evidence so that we can analyze what exactly happened here.
Update: I rewrote my whole post, forget the initial nonsense. I should not answer complicated issues when I'm tired.