I'd bet they are iron stains. To verify, put some vitamin c tablets in a sock, crush them with something, and then place the sock on the stain and leave it there for 5-10 minutes. If the stain lifts or lightens, you can clear it up with an ascorbic acid treatment. It's not very difficult, but it does involve some key steps. They include:
1) Test pH and adjust down to 7.2
2) Let your FC come down to near 0.
3) Add ascorbic acid to the entire pool walking it around the perimeter and broadcasting it toward the stains as well.
4) Add metal sequestrant to the water to keep the stains in solution once they are lifted with the AA.
5) Slowly bring FC back up near your target until the FC starts holding
6) Add a maintenance dose of metal sequestrant monthly to keep the stains in solution.
Depending on how warm it is in your area when you do the treatment, it can be risky to let the FC drop all the way to 0. If you add the AA before the FC gets to zero, it will just eat away at the rest of the chlorine before going to work on the stains. You'll just use more AA. You probably should use between 3 and 5 Lbs of AA depending on how bad your stains are. I used around 6 pounds last August in my 20,000 gallon pool, with my FC at 2 when I started. Let the AA go to work in the pool for a couple of hours to lift the stains. Then add your sequestrant. I use Metal Magic by ProTeam. I'd go with 2 bottles (quart). That will keep the stains in solution in the water and not allow them to end up back on the plaster.
When you start adding back in your FC, you have to be very careful. Add around 5-6 PPM of FC and monitor it closely. The FC will get used up very quickly as it kills the remaining AA in the pool. Check it every couple of hours at least, and top it back up to 5-6 again. You will go through a lot of chlorine until the FC starts holding. Don't be alarmed. Once the AA is gone, FC will finally start holding and you can get back to your target levels. Just be careful not to approach anywhere near SLAM FC level because that can cause the stains to drop out of solution and back onto your walls and floor.
Finally, you need to add a maintenance dose of sequestrant every month to keep the stains in solution. I add half a bottle (16 oz) and that seems to do the trick just fine.
Here's the AA I used:
5 lb Bulk Ascorbic Acid Powder | NewStore : PC NetwoRx Inc.
and the sequestrant:
https://www.amazon.com/gp/product/B01MYHDJNZ/ref=oh_aui_detailpage_o00_s00?ie=UTF8&psc=1
The 4 pack is the best deal.
