The plumbing code requires separate restrooms for men and women in restaurant/food service occupancies. I know owners often switch to one restroom being private for employees and the other for the public but that is done after the C/O is issued.
My state has a size exception. Restaurants with occupnancy/seating <15 can have a single bathroom. And the health code doesn’t say squat about ADA compliance.
This is why it’s really important to not let inspectors swan in and tell you things without providing documentation of the applicable code. They may be making stuff up or flat overreaching their authority. The health inspector doesn’t get to enforce the building code.
If she got all the applicable permits, why was it never mentioned during the permitting process? She needs to make sure that the “inspector” was legitimate, code violations come with paperwork. They have to document what is wrong and how it is to be corrected and by what date (because they have to come back and check)
Seriously, it could have been a contractor trolling for work or the pizza place engaging in a little competitive thuggery.