By discovering the problems yourself prior to your SQF audit, you should be insulated from taking it as a finding in the formal audit. A small scale comparison would be rodent activity discovered during the audit is an automatic finding, yet rodent activity noted in your logs with corrective actions taken will be documented as compliant with the relevant code.
Same thing should apply to an FDA check, though if the finding is serious enough it can cause a citation or other action.
But the whole point of a good quality management system, run by properly trained personnel, is to catch these types of problems before they spiral out of control. You've discovered opportunities to improve the procedures around these processes, the methods of which you're going to be able to document in your root cause analysis. Find out how these things ended up being swept to the side, and implement real change to make sure it won't happen again.