This might help:
http://support.chess.com/Knowledgebase/Article/View/91/13/why-did-the-clock-times-suddenly-change-the-clocks-seem-broken
Most likely, this is the result of lag. Your move gets registered on your computer, so it "looks" like you made your move, but it takes too long for the server to recognize it. Chances are, if you look at the game in your archives, either your last move wasn't registered or there was a move from your opponent that you never saw.
I make a move, it gets reflected among the game's moves, but then I lose on time. How can this be?
If I play out of time, then my move is not valid, and shouldn't make part of the moves of the game. If it's valid, then it's my opponent's turn, and I cannot lose on time -not yet.