fori,
Let the pool finish filling. Then you can use the pool brush to remove the stain. If that doesn't work to remove the stain and your pool is white plaster, you can use a piece of wet/dry sandpaper(80-100 grit) to lightly sand the stain out.

Thanks Geek. It's full and white and the stain doesn't brush out. Sandpaper sounds good!

We had stuff stain our plaster during fill, leaves and some dirt. Once chlorine was brought up to 5 ppm after fill all the stains went away, organic in nature.

Thanks Goyom--I'll wait, and if the chlorine doesn't take it out, I'll get abrasive on it!