There's also the matter of the second acid wash. It's possible to do an acid wash well, but any acid wash reduces the life of your pool's finish, and that's a fact. The first one, if done correctly, was supposed to be just aggressive enough to skim off the plaster just enough to reveal all the pebbles. But whatever pebbles were at the correct depth after the first wash might now have been compromised by getting washed again while the worker was trying to reveal more of the buried ones. The process they likely used is not precise enough to spot treat like that.
Acid washing is always the go-to move when a contractor fails to achieve a great finish the first time. It's really the only thing he can do (quickly and inexpensively, that is) to try and make up for inconsistencies. But acid washing removes plaster, and it is the plaster that is holding the pebbles in place. Too aggressive a wash, or a second wash, can weaken that hold, and unfortunately for you, the damage done (if there was any) might not reveal itself for many years (after your warranty has expired).
Is the water too cold now to get in? Once filled, it's going to be tough to see what they did or didn't do. Getting in with a mask or goggles and inspecting the finish would be prudent. Otherwise, you might get a nasty surprise next summer when the sun is up higher.
Sorry, that's all worst case. It's hard to tell from your pic if that's what has happened. But I wanted to share that so you might better know what to look for, and to have some ammo for your next conversation with the contractor. If he can do a quick wash and get you to accept it, he'll be long gone, along with your warranty, should anything go wrong years from now. It's not just a matter of cosmetics, longevity might be at stake, too.