I was playing a game and had the guy in a tough position. He let the clock run down from 20min to zero and got the points, even though it was his move and I still had 20 min left on the clock. My rating went down 13 points because of that. It's messed up. Does this happen often?
Really? 
you only lose points if you forfeit on time. it doesn't make sense that you lose rating points if your opponent loses.
As Dio said, and you may have been completely offline without realizing your screen had never updated you with a move your opponent made 20 minutes earlier.
There is a problem with time cheats on all online games who disconnect to preserve their time while yours runs out and then reconnect. Some sites use a "Claim win on disconnect" button that works if you continuously keep pressing it until you are awarded a win. I have had success with this. In spite of the gurus who say you can't cheat on time in chess it happens all too regularly. I would suggest the gurus are cheating themselves.
I too have clock problems, and they always seem to occur when I am winning. Just today, I was moving quickly, and next thing you know, I am down big time on the clock. Also, right before my eyes, the clock is adding time to my opponent. Is this a lag issue, or is their something fishy going on here.
I also regularly think I have clock problems. I realise most of the time I just don't pay enough attention, although there are cases when I start shouting at the screen that I played before the time ended. But then again, I have at least once been left with 1.6 seconds to play, when the time control is 5|2. Which is simply wrong.
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I was playing a game and had the guy in a tough position. He let the clock run down from 20min to zero and got the points, even though it was his move and I still had 20 min left on the clock. My rating went down 13 points because of that. It's messed up. Does this happen often?