You need to ensure that your business avoids any retaliation against employees who are participating in protected activities. It is easy to understand that a manager might get upset when a complaint is filed against them for something like violating wage and hour laws or harassment laws -- but they can't be permitted to act on those feelings in a way that could be construed as retaliation. Under the bounds of federal law, retaliation is something that can lead to litigation against your company.
Everyone in your company should know the definition of retaliation. In its simplest form, retaliation is somehow negatively affecting the employment of someone in response to their protected activity. This can mean an employee is terminated, gets a pay cut, sees a drop in hours, is moved to a less desirable shift, is demoted or is passed over for a promotion they were due because of whatever they did that provoked the ire of their superior.
Some protected activities employees have a right to pursue include filing a complaint about harassment, discrimination or illegal activity. They can also cooperate with an investigation about those activities. It also includes failing to follow orders that would result in illegal activity, resisting advances from people they come into contact with for work or taking steps to stop others from becoming victims of harassment or discrimination.
If you find out that an employee is alleging retaliation, you have to start thinking about how to protect your company. Having a strong stance against retaliation and being able to show that your company is proactive about educating managers and supervisors about what constitutes retaliation versus legitimate disciplinary action can help insulate your company somewhat from litigation.