Nonconforming parts should never be submitted with a PPAP unless the customer has explicitly allowed it, in writing. You don't ask for a deviation or waiver with the first submission of a PPAP....anything that doesn't meet the requirements must be flagged to the customer and a deviation sent pending a final disposition agreement - like either correcting whatever is causing the NC or updating a print to match the NC condition. The PSW that you are signing as part of the PPAP is a legal document that says you are presenting these parts to the specifications. If you don't note on the PSW that there are problems, then you and your company could be held legally responsible.