1) Handbook states 3 or more days need a Dr's note. My department needs one if you miss one day
2) Handbook work attire, if every other department can wear certain appropriate outfits but 1 department manager wont allow their employees to wear them and makes comments
3) Handbook Open Door policy on HR Department, however Boss tells employee that they will get introuble for going to them or it was innappropriate to go HR department for specific reason
I don't know the relationship between "your department" and the "company." Maybe your department has its own rules, which it sounds like. Are you paychecks from the company? If so, you need to explanation why your department seems to be governed by its own unwritten rules.
A company needs to adhere to its own rules, and if the employees don't know them, it's hard for the employees to follow them and for the company to enforce them.
You either need to see your HR department to get clarification on this, or see your own lawyer.
I'm only licensed in CA. Please note that this answer does not constitute legal advice, and should not be relied on, since each state has different laws, each situation is fact specific, and it is impossible to evaluate a legal problem without a comprehensive consultation and review of all the facts and documents at issue. This answer does not create an attorney-client relationship.