I am wrapping up a thorough renovation to my home. I have a GC who used a sub for the hardwood refinishing job as part of my project. My floors are red oak.
Floors were completely sanded and refinished with a medium brown stain color and two coats of water based poly.

The first time they refinished them, they did not buff and clean the floors. A two week window had passed between applying the stain and the poly coats (as my GC requested). They applied the poly without buffing and cleaning the floors, trapping debris and paint on the surface of the floor, but below the poly. It looked awful. They came back and tried to fix it, but there was still paint everywhere.
As a result, the GC and the sub decided to completely sand and refinish again.

Now, here is my question - on this third overall attempt, and second complete re-do, they did not remove the shoe mold that was reinstalled after the first full refinish. They sanded, stained, sealed, and applied poly with the shoe mold still attached to the floor. Is this right? Now my floors look like they have a gap between the bottom of the shoe mold and the floor surface because it is so dark. The GC and the sub (I met with them yesterday again) are saying that it's fine and that this is common. They say the shoe mold didn't have to be removed since it is the same color stain. There is also bubbling in the finish in spots (but no debris). He said that would dissipate over time.

I am not a hardwood expert, but from everything i can read online, shoe mold should be removed, with base board removal as optional. I can't seem to figure out how to upload pictures on this forum, so if anyone wants to see what I am talking about, I can email them.
In the meantime, please tell me if this is acceptable, not acceptable, if I am over-reacting. I have spent so much money on this project, and i feel like my floors are ruined.

It is common to not remove the base shoe when refinishing is being done. There can sometimes be a "shadow" where the shoe and floor meet if the shoe does not conform perfectly with the floor surface.
You may need another coat of finish applied to make a smooth floor. Most waterborne finish companies recommend 3 coats for a heavy traffic area. This will make the floor easier to clean and last a lot longer.
Did you have a contract for the refinishing or did you see specifications for the work?