Competence is a status of capability in more than a technical sense.
Many brilliant engineers, doctors, and other subject matter experts can still render their responsible processes ineffective through a less than optimum allocation of resources--both material and human.
If your engineer is not able to apply management methods such as the Theory of Constraints (see here
http://www.nysscpa.org/cpajournal/1999/0499/Departments/D530499.HTM ) then arguably an inability to harness technical prowess into the output of his responsible processes is a practical meaning of incompetency.
This is a very common event. While line operators will have elegant training programs designed to manage their output through skill development, very often this is not done for engineers. Engineers who are very skilled in theory may bumble when performing their work according to the plan because the theory naturally varies among learners and the education sources.
So I encourage you to now only categorize the education and experience in all persons operating in your processes, but identify gaps they may have in being effective at applying their learning. Teamwork, problem solving using cause-and-effect, project planning and assessing results are, IMHO, essential elements of most any competency set and may help your engineer to better articulate his understanding of the system and appear more adaptable. I say
articulate and
appear because the auditor may have based remarks on what is seen. If your engineer possesses capability he didn't display to the auditor--perhaps by just not providing the answers or evidence needed to convince the auditor of competence--the verdict was delivered as a CA. I do not know your engineer but I do know that sometimes the problem is not incompetence, but underperformance.
I hope this helps!