I can't tell from the picture but are they brown or rust colored?

I get similar spots in my PebbleSheen. Pool builder says it's a mineral leeching out of some of the stones. It always happens in the exact same spots. I've got about 9 dime sized and smaller spots that will reoccur a couple times per season. Tried everything to remove them. The only thing that worked, like magic, was absorbic acid. In other words, I had my 14 year old swim around, underwater, with a mask on and rub the spots with a simple Vitamin C tablet. 1000 mg.

I saw one post on here, where the pool got brown stains in the same spots but they were long. Turns out the rebar was rusting through the pool finish. Yikes.

Thanks for the message, banana. I've have metal stains which come from fertilizer from the adjacent golf course. These clear up really well with a handful of ascorbic acid, no problem. But the cruddy spots I have are actually nodules about 1mm above the surface. They don't have any distinct color, just dark. Like I said I can sand them off and they're gone and the surface looks perfect. I just don't get the position memory - every season, the same spots.

Here is a good place to start for stains see links below. You may want to try a test kit.

Hope this helps
Rusty

Here is a link that might be useful: Jacks Magic