I'm not sure why it happens but I have noticed that whenever I double-click on the play link there's a good chance that an extra puzzle will be in my recent games list. Yesterday I noticed that I had three games I didn't know about and I don't remember double-clicking.
By the way, I'm using Firefox also and don't know if that's a factor. And although I love using Firefox, one thing I'm not crazy about is that it shuts down on me from time to time. When that occurs while I'm doing a cryptogram, the next time I open a browser it opens with a different game already in progress, and the seconds are ticking away. Then I have to go back and complete the puzzle I was doing before the crash.
I try to check statistics after every game. It slows you down some but at least you know right away if you've missed one.