OP is a manager, good managers look out for their subordinates and surface issues so that they can be solved. Ideally before they become thorny legal issues. From this write up, it looks that OP did exactly this. At the beginning, she surfaced issues with two employees that could cause problems down the line for the company, she highlighted potential issues with documentations, requirements and test cases that would be problematic with the FDA (in any highly regulated environment like medical devices, making sure that the company is compliant is crucial and definitely the responsibility of any project manager).

So, she did exactly what she was hired for.