I'm more a ISO9001 person than a "AS9100, IAQG, NADCAP and Aerospace related" however I've done extensive audits of many systems of many organisations to many standards. Some things I would consider.... When you write your audit finding will it be categorised, such as "just an observation they they can choose to ignore" or some kind "noncompliance" (against a legal instrument) or a "nonconformance" (non legal instrument)? If you can't call up a part of the audit criteria in your adverse finding then I'd think about the category more.
Then as some have mentioned.. risk based thinking.
Organisational context plays a role too. It reads you are auditing "their" systems and that you are external. So what are your own real risks? Well, you're taking some risk if you choose not to mention this cap thing. So the answer is raise it and choose your category. "Consideration could be given for the organization expanding an existing documented risk assessment that demonstrates what does and what does not require traceability. For example risk relating to caps blah blah blah." This way you are encouraging them to go think about it and in some ways it's a transference of risk. They should be the experts on caps, and if you're worried that the risk can be higher than some might presume, mention something about checking their mitigating controls for "cap related risk" with their insurer.
Or if if it is noncompliance or nonconformance, just write it up and quote the clause(s) it conflicts with.