Definitely do the trichlor puck and vitamin C tablet experiment first.
However, I would like to offer a *possible* explanation - I believe those stains in the Pebbletek originated from the final acid wash etch step after the pebbletec was applied. The person doing the acid wash probably hit those lovely stones and etched some of the minerals from those stones onto the newly exposed Pebbletec plaster. Depending on the composition of those stones, the stains may or may not be removable.
And how might I suspect this? My pool has some very similar stains in it right under the rock waterfall and they neither grow with time nor are removable with trichlor or vitamin C. I asked a friend of mine that does hardscape work what he thought and he surmised that the PebbleTec crew did a sloppy acid wash near the stones. They use a high pressure washer with acid to reveal the Pebble aggregate. If they are a careful crew, they will cover any stonework to protect the pebble creme (plaster). If they are trying to bang out the job too quickly...well...accidents happen.
I hope your stain is easily lifted! If not, considering how new the pool is, I don't see any reason why you can't contact the PB and ask him to rectify the stain. It is not your fault and you deserve to have a beautiful pool.
Good luck!