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Problem with paint, like anything else the stain will eventually come back unless you find the source
Rust stain. This can be caused by a few things. But both are from metal.
When troweling the walls to complete the finish if the contractor failed to use stainless
Still another reason for a rust stain is that the rebar used to construct the pool has become wet due to poor construction and failure of the plaster coating on the wall to keep the moisture away from it. As moisture hits the rebar, or even the wire mesh within the cement it too begins to rust and this rust begins to seep out of very tiny cracks on the surface of the plaster coat.
In any case you can clean this rust by using any good quality rust removing chemical purchased over the counter. But this is only a temporary fix. You must find out what is causing this rust and correct it, or its only going to come back.
Now if the stains your speaking of is sort of a white colored line that has begun to develop on the walls. That is a sign that water is effecting the plaster coating on the walls of the pool. then I would have the water checked first as using to much chemicals or in some cases not enough can cause all sorts of ugly things to happen not just to pool, but to filters, and other attachments connected to the pool that sees the same water.