A similar thing happened to me. I have sent some coins to address A only to see some more sent at the same time to address B. If I understand correctly, I also control address B so I haven't lost out. I am using bitcoin-qt under linux. Is there a way I can see inside my wallet to confirm that I control both of these addresses? I don't doubt the integrity of bitcoin, I just want to learn more.
Not sure where you can find it in the linux version, but bitcoin-qt has a Debug Window with a console (in Mac it's under Help - Debug Window - Console). Open it and type
validateaddress . It will show some information and if it shows "ismine":true it is your address :-).