It's difficult to see what you mean, but I think it's the gray shadowy area in the center of the threshold running lengthwise? If that's it, it almost looks like you might have mold growing under the threshold that is showing through...tho' how that could happen is a bit of a mystery. I can't really tell from the picture, but on the inside of the shower, is the inside edge of the threshold just a solid piece or is there some kind of a strip attached to the larger piece? It almost looks like a seam at the top edge and if it is, water could be leaking through there. Or is it where the shower door sits? If that's it, the stone could just be holding moisture from the bottom of the door (or is being stained by the gasket). If you leave the door open between showers, does the stain lighten?

it is a long strip of stone(not sure what kind) about an inch or two thick. There isnt really a seam, but the shadow is darkest on the edge of the threshold which is maybe what is making it look like a seam?

Leaving the door open doesnt seem to make much of a difference