It didn't work against supergirl the boss after 40% hp right? If so or just in general the way it works is that is you have anything else that increases damage like after you do a supermove or what not or if the opponent has anything the decreases your damage the mod won't work because the extra super damage is over riding the mod extra damage. Sorry if I explained it poorly but basically mod doesn't work unless you have nothing else affecting your damage
Oh, it's definitely working. It's just that she has a passive which activates when her health dips below a certain point and cuts incoming damage by 40%. To finish her, you need much stronger damage dealers. I'm in the same boat.