If they ask about customer service and employees behavior in the report, I write about it. It is a job, where I have to report both positive and negative observations. The employees are paid to do their job, I'm paid to observe them, if one of us is not following the guidelines than we shouldn't do it in a first place.
Sometimes companies don't ask about customer service like recent Subway shops, where they only cared about quality of sandwich.
There are also times when MSCs remove negative observations from the report and low the grade, well, in this case it's on editor, I did my part following guidelines from A to Z.
As for feeling bad reporting inappropriate behavior, I don't feel bad. It's a job, I don't think police officers feel bad arresting criminals although it hurts criminals' families.
I personally like when reports have a section asking my personal opinion about a shop, I share my thoughts there, and the rest of the report is written in neutral nonjudgmental language, just pure observations.