It might be from inside the concrete, such as wire ties that were left too high and are bleeding through, or it might be something metal that got into the pool.
Some possibilities:
1) If a wire brush was used in or around the pool, bristles might have broken off and caused iron stains.
2) Using steel wool around the pool.
3) Cutting steel around the pool can leave metal bits.
4) Hair pins.
Try scratching them off with something hard and sharp. But, be careful not to gouge the plaster. A clean, smooth stainless steel knife usually works well. If the spots scrape off easily, then it's introduced contaminants. If the spots do not scrape off, then they are likely to be coming from inside the plaster.
Note: Wire ties are the wires used to tie rebar together at the intersections.
If you're still not sure after trying the scrape test, a picture might help us determine what the cause is.