What I see is people not understanding specifications.
A drawing say install rivets per NASM41799 (I'm sure that number is wrong) or something like that and the spec says use TTP-1757 paint, and your assemblers use something else, and it is out of shelf life.
Major
Doc control
The assessor walks in, your quality policy in the lobby is Rev. C. In the conference room, for the opening meeting, it's D, and on the floor, it's B. The first shop traveler is Rev. A and the Drawing is Rev. NC, and the instructions say they got to match. Assessor finds 2 more travelers like that.
Major
Inspection records
Assessor asks the inspector for their records of inspection. The dimensions are out of tolerance. The part is about to be shipped, signed of as conforming.
Major
Basic system tools
You have no records of Management Review, or maybe Internal Audits, or you have 60 open, overdue corrective actions.
Major
Misc...
Your biggest customer complained about a major safety issue. There are no records the organization is responding...
Your objectives are all under goal and there is no record of action or correction...
Your secret side business, advertised as under scope of accreditation, is discovered during the course of the assessment in the building across the street next to the Subway...
Your material certificates show chem and phys results that don't meet spec...
Your are working for Boeing but not heat treating with a Nadcap processor (without a deviation)....
You are outsourcing painting for Lockheed without flowdown of the Lockheed paint spec....
I could keep going.