It could have been a lag or maybe you made a mistake of mistaking milli seconds and seconds
CHESS.COM - Serious mess up on time
Yeah, lag sometimes does that. I remember one time I was playing against my friend in the same room (college library), the friend's clock would be ticking down on my browser but my clock would be ticking down on my friend's browser. The server apparantly did not register my last move because of the library's crappy connection. We waited for about 3 mins, after which the clock updated and I was 3 minutes down and 3 minutes was "added" to my friend's clock.
:(
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I was winning a game by a great deal on time. Next thing I know, my time is at 0 and the other guy wins on time. HOW IS THIS POSSIBLE WHEN I HAD OVER 30 SECOND MORE THAN HIM AT THE END? ARE YOU KIDDING ME?!?!?!