Like Billy, I've done the double clicking before too. The only thing that saves me is that I scroll down and check every card after I enter it in my collection to make sure that it's in there. That's definitely a possible explanation,
It could also be a site glitch. Those do happen.
A third possible explanation is the trading, as mentioned above, but if this card wasn't involved in a trade of any sort, then this idea is ruled out.
A fourth and final idea is that it was a simple mistake - perhaps you thought you had two and entered it twice. I've also done that myself. Annoying? Yes. Fixable? Absolutely. Like someone mentioned, you can easily remove that second card from your collection by unchecking the box, or by using the dropdown menu next to it and selecting "Remove from Collection"
Hopefully this helps; if not, I'm afraid that I still don't follow your problem. Best of luck!
Jason
I'll never quit collecting entirely, but I am downsizing. Check out my COMC store and help me thin out what I don't want so I can buy cards that I do want. See something you like? Send me a message on here, and we can knock the price down quite a bit. I'll even take a bit of a loss if it means getting you a card you really want.