Yes I have had that happen, a few nights ago as a matter of fact. (I sent a note to Admin about it.) I completed a puzzle and was notified that it had been initiated by a registered user. Somehow, after I started that puzzle I was logged out. I noticed some time later that my score was below 100%. I checked the Recent Games list and the unsolved puzzle was listed there -- it turned out to be the same one I was doing when I was logged off, even though I had completed it.
Perhaps something similar happened to you. The only disadvantage to me was that my solve time really went up -- it had taken something like 2300 seconds for this puzzle. It might be a good idea for you to check your score before you log off and make sure that it's at 100%. If not, go to the Recent Games list and find the puzzle that was missed. The cryptogram site gives you 120 minutes to pick up any puzzles missed, but you have a much longer period here -- I think it's 24 hours.
Hope this helps!