its kinda like a glitch i believe. it happened to me too. u placed ur piece after u loss/the timer goes by too big of an increment to allow .01 seconds.
I checkmated but I lost!

it also happened to me several time.my time already finish but i can checkmate him with one move only.he can' do anything.

When a game is over, the board is automatically switched to analysis mode. Look here: http://www.chess.com/livechess/game.html?id=10578473 , your move was not registered.
I checkmated my opponend but I lost on time. I had already done my move.
Check this out