Who is the GC? Is that you - or is there a GC in charge of this job?

If there's a GC - talk to them and find out what is going on. Is there a drawing or diagram of what it's supposed to be? If there's an adjustable bar on the left, It's possible that everything is fine except for what I presume is the tub spout - but I don't really know without a diagram.

If YOU are acting as the GC, then you are about to find out why that's a bad idea.

Here's the thing: You shouldn't be discovering that the plumbing rough-in is wrong once the tile is up. It's the designer's job to produce a drawing or diagram of the where the rough-in should be. An experienced plumber will know better than to wing it. And it's the GC's job to be sure it's right before the backerboard goes up.

If this is messed up, it's going to be a tear out most likely. It's very unlikely that you can fix the rough-in without damaging the waterproofing behind the tile. It's also unlikely that you will be able to do a localized repair and have it be satisfactory. If you had full access to the back side of the plumbing wall you MIGHT be able to pull it off... but you are probably looking at completely removing the backer board on that end wall. Doing that means that you will be taking off the tile on the window wall at least a foot or so from the corner so you can get the waterproofing in the corner done properly once the new backer board goes up. If you are very lucky you can tile it back from there.

Again, if this is wrong, several people dropped the ball for it to get to this point and it's going to be expensive to fix.

Thanks Jake. I wanted to provide an update.

1. The tub spout hasn't been installed.

2. The middle piece is the hand shower - this is wrong as I don't have a hand shower and plumber did not ask what the trim I planned on was.

3. The lower valves are for the thermostatic trim. I think this is too low but may not be worth changing out at this point.

Okay, so you are saying that the hole for the tub spout was covered over? That's a lot easier to fix - and makes a little more sense.

It will probably be better to install a hand shower now than do anything else with that rough-in.

Thanks again.. I think the issue could be that the valve doesn't accommodate a hand shower so it may be cheaper to patch the hole than buy a new valve, handshower, and trim - all of which would be needed to switch to hand shower. My GC has been extremely absent but it's complicated. I'm getting a great price and would be stressing about money if not the plumbing.. pick your poison, I suppose. Fortunately very close to being done finally, and learned a lot being more hands on. My first project was in a different circumstance when I had more funds and it was nowhere near as stressful, but you pay for what you get and you get what you pay for! Grateful to Houzz and commenters like you for the advice.

Would you mind sharing what marble that is? It looks great.

Thanks, it’s Builder Depot Venato Carrara. Daltile Contempo has a similar but whiter look, while I’ve found Jeffrey Court marble from Home Depot is notably greyer. Hope that helps!

My bet is you're getting a handshower and when it hangs in line with the others it will look fine.