Again, it would depend on whether or not we get co-operation from a department. If it's senior management that doesn't want to collaborate, we'd certainly mention that in our report. However, we usually receive incredible collaboration from all departments.
That said, I've been an auditor for almost thirty years. Over the course of my career, some individuals targeted for audit have failed to provide us with the required information, whether accidentally or intentionally. In such situations, it's what you do afterwards that's important, in my opinion: as an auditor, how should I approach the situation, and how should the individual approach it? We certainly see this from time to time in our audits.