No, it is not possible for a player to manipulate the time as you suggest. This appears to be a lag issue and connection issue that you or your opponent experienced which made it appear that the times were not correct.
We have programmers working very hard on these lag and connection issues in the Live Chess which will hopefully be resolved very soon!
When you are playing a real time game, can you set the time limit for you to have more than your opponent? some guy's time limit kept resting when he moved but mine did not. i only had 1 minute to move and loss because of that.