Are you talking about a standard clock live chess game?
Part of the problem is internet lag which is beyond chess.com's control. But I know, it's frustrating to see your opponents clock run to 0:00 and then poof! Suddenly he has 15 seconds left, to your 2 seconds.
There must be a way to fix this.
Instant update of opponent's clock when it is your turn rather than a countdown.
I notice for several occasion now especially in the end game that the clocktime is manipulated by my opponents. Is it possible that the clock time can be adjusted for several times especially in the end game just to avoid losing on time? The worst is that you can not move your piece as if moving is illegal, is this possible? If possible, why??? Its very discouraging sometimes.