What likely happened is that you had a brief disconnect and the server may not have received your move.
The server is the keeper of the accurate time. With the lag compensation algorithms the times on the clients may not be accurate. That is why you may occasionally see clocks adjusted in games, even without increments.
Could sb. tell me why the clock in some games does not count down to 0? I have just played a 5 min game and the clock just has given the other guy at the end seconds so his game has not endet (but mine....).