So, these major and minor nonconformities that exist in your system, did you point any of them out the the external auditors when they were there?
OK, so you may say that it is their job to audit the system and if they spot anything wrong, to point it out to you but if they are sleeping their way through the audit, why note tell them about the problems and let them raise them to your top management.
Better still, why not fix them anyway? It isn't mandatory to get an N/C before fixing a situation.