This can sometimes happen when your computer is lagging - you can't really help this other than getting a better connection sorry :/
Time system for online matches
Sort:
https://support.chess.com/customer/en/portal/articles/1444849-why-did-the-clock-times-suddenly-change-the-clocks-seem-broken-
You could also be seeing a symptom of disconnection:
Hi there! The time running system of the online matches made me lost some games unfairly during the time i ve been playing with chess.com. Basically, when the match is coming to the end, the opponent starts getting bonus time to stay alive in the match, without explanations