Our pool has a Black Onyx Pebble Sheen interior, which we really like. Having said that, and adding that I am not a pool company owner/employee -- just a homeowner with a pool, I will say that the holes in the finish are not "industry standard." Neither is the excessive color as shown in your photos.

As for the holes -- the company should come out and fill them in with additional Pebble Sheen.

As for the color -- it appears to me that the acid wash wasn't done properly. Since your pool is now being filled (is likely already filled by the time I'm typing this), the company should use the handy-dandy acid applicator that will apply acid directly to the necessary areas and then brush it to get rid of the excess color. By the way, the excess color isn't really "excess" color -- it's just the stuff that wasn't acid washed/brushed away. Think back to the day when the Pebble Sheen was applied. It had to sit and "cure" for 24 hours and then a crew came back to buff it and acid wash it. They simply didn't do a good job with the acid wash.