We have had zero issues with the machine since it has started up in 2015. I think they were expecting to see a 30-40 page report outlining the reasons for the exercise, reason for sample size etc..
Yep, statistical reasoning behind sample size would be required. An IQOQ wouldn't require sample size, so you must be referring to a PQ.
So the finding wasn't that PQ didn't exist, it was that it wasn't completed well. Validations have grown in the 20 years I've been doing them. Medical device company's are now expecting a lot more, including a risk analysis and links to each test that would reduce that risk.
Did you write the protocol first and have it approved before completing the testing?
Very few suppliers have the experience to write thorough validations. Yet the purchasers demand them. Typically this results in useless documents that only exist to fulfill a customers checklist.