I have learned a tremendous amount from this forum. I would like to contribute by sharing my experience with a dark spot or stain.
Soon after plaster and filling, I noticed a dark spot on the bottom of our pool. The pool builder tried to pour acid on it through a pipe and then lots of brushing, but that didn't make a difference.
The pebbletec installer came out and said it looked like a "hydration stain". He said acid would only make it darker. He recommended draining the pool, allowing it to dry in the sun for a few days, and then heating the dark area with a torch to "dry it out". The stain really bothered me so we decided to go ahead and let him try to remove it.
Here is what it looked like with the pool empty and dry:
Here is what it looked like after torching and filling. I cannot see the stain any more:
I believe this was caused by water pooling on the surface during and after the power wash of the new finish before the pool was filled. There is a low spot on the floor and this allowed water to pool. Since this is in the shallow end, water probably sat there for hours as the deep end filled first. This is why it is so important to fill the pool without stopping, to avoid the "bathtub ring" that is caused by hydration of the new plaster at unequal rates.
I'm posting this so others can see what a hydration stain looks like and be aware of the way to remove it. Importantly, according to the pebbletec installer, acid can make these stains worse, or not do anything at all. The pebbletec installer knew right away how to deal with this, but the pool builder wanted to keep adding acid and brushing. I hope this information is able to help someone with a similar problem.
In these pictures you can see the low spot in the shell and how the water was pooling in that spot when the installer was working on the deep end.