That's how it's supposed to work. If there is a period of a match where one player would require a lot of time to think, fight connection issues and/or calc hits, it wouldn't be fair to leave them with only 50 seconds to battle with for the last 15 turns of a 20 turn match, just because they took long time to decide in the first 5 turns.The timer in random battle needs to be fixed. You know how when someone stalls the timer until it says "Username has 10 seconds left" for the first turn it cuts 30 seconds off their next turn when they stall again, but then they play normally for the next two turns after that (3 and 4) and it gives them some of their time back so they can stall even longer. It shouldn't be doing that.
Of course, that doesn't mean timerstalling is OK. It's just that finding a system that leaves room for thinking time without leaving it susceptible to timerstalling that everyone can be happy with is pretty much impossible. If your opponent is excessively abusing the timer, I suggest that you report them to a global driver or higher (users marked with a @ in the help room).