No, I have never had any negative impact from flatworms. I do however think they are horribly ugly.
I have been holding off on a few things for when I feel the tank is stable.
I like a refugium full of algae before I consider my tank forgiving
So, I think once the fuge is fuller I might dose flatworm exit. I have had good success with this product in the past and never had any side effect I could notice.