Tag Team Assault
It might sound obvious, but it is a two on one fight and the hero side should exploit that. Ruthlessly if they have to. If your timey-wimey guy can only effectively affect one area at a time, then the solution is the two people not being in the same area so that they can't be hit at the same time.
One person might be frozen, but that leaves him vulnerable to the other guy coming up behind him, possibly from a blind side. When the antagonist lapses on concentration to deal with the second person, that frees the first.
It feels like this battle will be more than just a straight out super-powered slugfest, but something where deeper bits of strategy and tactics will be involved. The villain would have the goal of getting both into a single spot that they can time stop, which should end the fight there. The heroes need to maintain positions to prevent that from happening, and potentially save their comrade should something bad happen to them.
Smoke creation could be used to blind and/or suffocate the villain, depending on the control over said smoke and any ability to dispel it once it has done its work.
Timey Wimey Powers
The main drawback of this power in my example is that only one area and effect can be active at a time. So while the flow of time can be altered in an area, it is constrained to one area and one temporal rate at a time.
The obvious weakness is perception -- they need to perceive something in order to time-whammy it. Whether that is an area of space, or a person, or themselves, they will need to be able to perceive it. As we are a visually oriented species, this is likely based on sight.
Of course, if this isn't super-serious … or you have that kind of character, just lay on them a giant tirade of spoilers for their favourite shows. Their desperation not to know might lead them into making a mistake in their drive to not be spoiled. If you can go on for long enough, they can't timeslip back out of it.