Unfortunately there exists a messy side of company culture in which perception (by peers and management) impacts morale and performance. In a utopian company, all employees are judged purely on their productivity and have unilateral say in their working conditions. Unfortunately our world is filled with people and their pesky emotions. People get upset when they perceive unfair treatment, and things like "good reason" and "productivity" can be so subjective.

This is a matter of nurturing a good team culture. Culture is hard.