The rejections are for some marks on the paint that expose the primer and for FOD/dust specs under the paint. Not every part has this issue but the entire lot is rejected. The question is to what can we use to hold our supplier accountable to for the paint?
First, contact the supplier and discuss the issue. Exposed primer and FOD/dust under the paint are common issues that even if not specified in the contract are standard 'understood' nonconformances. If they have any credibility they're not going to argue. Whether you reject the lot or not is an issue, but it will come down to who does the sort, and where, and who bears the cost of the sort, assuming all are not bad.
My opinion is based upon a number of years of working with companies in resolving cosmetic issues, from paint(s) to screen printing to anodize, of metal, injection molded and parts of other materials.
I remember a problem with a Honda part in one company which argued that the defects ('pinpoints' of exposed primer, mainly) were on a cover for an engine part where the the defect(s) were on the inside where the end user would never even see them. Honda would not yield - Their position was a defect is a defect and there was no exception just because the area would never be seen.
Typically boundary samples are used for determination of accept/reject.