I find when you too many negative comments are made about an employee, even if true, the scheduler emails for further information. I have, not had a shop rejected for negative comments.
However, I do agree, the more negative comments you have in a report, it does not make the company very happy.
When I know that the negative comments might be a problem, and I have a relationship with a mystery shop company, I call before submitting the report. In that particular instance, I do not have any further clarification emails.