[app woes] ... How do you write a characters abilities/nerf said abilities when they essentially can manipulate the universe?

Limit range.

When I nerfed Hex for MLJ, I declared that she could only manipulate reality if she was physically present to do so.

Oh, for this character they have to be in the area to manipulate reality. Canon is pretty spot on for that.

just, canonly another character with the same powers completely changed the world so everything was normal as sin.