Did it rain or did someone wash the decks down as the pool was filling?

I don't remember it raining that day, but it's possible. No one was around when it was filling. The company placed a hose in it and left for a while while it filled. I know they filled it right after they finished the gunite. These marks are all over. Some start below the light. This is a nature 2 pool btw.

Most likely it is scale caused by calcium build-up. Are you on well water? It is fairly easy to correct if you follow the recommendations of Jack's Magic (just Google them). You need to add a sequestering agent like their Magenta product and then use Stain Solution #2. It takes about a week of not using the pool, but should work. That's assuming nothing was done wrong during application. If the PB is willing to drain and redo, then it might be an application issue.

That is great that your builder is willing to come back out and diagnose the problem. They are correct in that they cannot give an explanation unless they see the problem before stating what they believe caused it. I would like to hear what they say. Keep us posted.

Here is a link that might be useful: Pool Plastering Contractor