As you probably know there are actually 3 clock times. Yours, the opponents, and the servers. So my guess is you had a temporary connection loss and your last move never made it to the server. Not a bad idea to refresh the page if your opponent is taking forever to move; he may have, but you didn't get it. I'm sure these articles will explain it better...
https://support.chess.com/customer/en/portal/articles/1444849-why-did-the-clock-times-suddenly-change-the-clocks-seem-broken-
and
https://support.chess.com/customer/en/portal/articles/1444918-my-internet-connection-is-fine---why-am-i-getting-disconnects-
Hope that helps...
I just lost a game due to running out of time; the weird thing is, it was my opponent's clock that ran out, yet the loss was charged to me! has anyone else had this happen?