I have recently been written Nonconformance's for what was deemed, "Auditor's Opinion"....The Auditor even admitted it...
I wont go into the details, but when the Auditor admits its his opinion he his writing you up for, you know something is wrong.....
I agree wholeheartedly with you that 3rd party auditing must be evidence-based, fact-based assessments and "opinions" should never be justification for nonconformities. That's what we are taught in Lead Auditor classes and those of us who teach Lead Auditor classes emphasize this aspect as well.
Not sure what standard you were being audited against, but, and very unfortunately, this new generation of ISO MSS's following the High Level Structure, are significantly more subjective than the previous versions, which leads itself to "more opinions" being interjected during the audit process. One needs only to look at the endless discussions about risk based thinking and what constitutes "evidence" of compliance...
Auditability of requirements is something that the ISO TC's were supposed to validate during the development process of the revisions, and, in my opinion, they failed miserably. This latest batch of ISO MSS standards is overly open to multiple interpretations and make the job of (internal/external) auditors much more complex and subjected to criticism, as in this case.
Not surprisingly, highly regulated sectors such as the medical device industry, the Aviation, Space & Defense sector and the Automotive OEM's either ditched the HLS or hugely augmented their respective standards to provide clear-cut, auditable requirements.
So, coming back to your feedback, while you are 100% justified in your expectations, the "new context" in which 3rd party auditors operate is different than before. As I have said numerous times here and in my LinkedIn Group, the management system conformity assessment practices have not been updated to reflect the new reality of auditing against HLS-based ISO MSS's, which, in my opinion, just shows the lack of vision and awareness by the IAF and the whole conformity assessment sector.