Misting twice a week with no leaf litter is almost certainly it. Box turtles want moderate to high humidity and substrate damp enough to burrow into properly, and in a dry enclosure the water dish is the only wet thing in the room. So she has gone and sat in it.
Get a hygrometer rather than guessing. Then deepen the substrate, mix in some leaf litter, and wet it down through rather than spraying the surface. Mine stopped living in her dish within about four days of that.