The billing companies I work for handle things as follows:
1. The staff/doctor is notified there is a denial for no auth/referral, and if they did get it, but didn't let us know, we submit a corrected claim with it. If they didn't get it, we go by what the EOB says...which is normally a write-off, and NOT patient responsibility. And we educate the staff on the importance of obtaining all necessary referrals/auths. We also try to have the staff get the auth/referral retroactively, but that is not always possible.
2. I let the client know about the denial, and refer them to the LCD for covered dx's. They then tell me what I can change the dx to, if in fact that patient has that dx. If not, whether we write the charge off or bill the patient depends on what the EOB says, and what insurance the patient has...meaning if it is Medicare and there should have been an ABN, but the provider didn't get one, it is a write off. While I have access to all patient notes, I cannot as a biller autonomously change a dx without talking to the doctor.
Obviously, in a perfect world, things like this would not happen, but they do, and sometimes a lot, depending on how educated staff/doctor are about this kind of stuff. In some cases, it IS the billing companies responsibility to run eligibility, etc, and tell the staff what auths/referrals are needed, before the patient is seen. It just depends on what services the billing company is contracted for with the client.