Probably a discrepancy with the code that handles lag. Server had you out of time and thus the game was lost on time even though the client allowed the move.
Though, it's also possible it is a bug in the implementation.
Incorrect rule implementation
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May 28, 2015
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#3
Server time is the official time, so this probably was a case of lag between our server and your system. I've mentioned this to the developers in case there are improvements that can be made.
Checkmate trumps the clock according to the official rules of chess.
In this game, which is fishy enough with no less than five disconnects by my opponent, I checkmated my opponent just as time expired. It should be a win, but chess.com awarded victory to my opponent.