Disconnects.
Sometimes the client shows the move but it never gets received by the server. It looks like your opponent's time is running but your opponent just sees their last move and your clock counting down.
If you are on the website you might try switching to v3 and/or checking out the following.
How is it possible that an opponent who is under check and not make a move still be able to eat what is left of my time and win? Glitz or cheats . . . happens all the time. I find it frustrating though funny at times . . . as that accounts for 95% of my loses alone. Not that I really care much about ratings.