You are not alone.
http://www.chess.com/forum/view/help-support/move-done-but-my-clock-keeps-running
Please use newest Web client and let me know if that happens again. It took some time, but we were finally able to install some related improvements to hopefully fix the issue. Thank you!
Why does my time rundown even though I've moved? I did'nt notice my time was still running, even though my move was recored by the server, and I lost. This is not the first time this strange bug showed up.