Debby may want to expand on this. From my own experience, I know of a local doctor who did go to prison for up-coding, coding for procedures that weren't done. Most of our graduates work for hospitals where the doctors aren't involved in coding decisions. If you were in a doctor's office (most doctors can't afford credentialed coders, so that wouldn't happen often) where you were instructed to code fraudulently, you would leave.
The situation would be more likely be a coder working for an outpatient clinic where the person in charge of coding isn't aware that they are under-coding, resulting in problems with reimbursement. There might be rejection letters followed by the Billing people having to make phone calls to resolve those issues and get payment.
Delays in payment are a big problem for medical clinics. If they don't get paid, they can't pay their own bills. This is also where you might hear, "We've always done it this way."
The doctor may have gone to a seminar on a cruise with lots of other doctors at some point where they were taught to code a certain way, even possibly using a Superbill where things are circled with little thought or effort. At that time that may have been the correct code but, as you know, things change. Doctors don't always update the coding skills related to their specialty or sub-specialty, so they may not be aware that anything changed. They will probably eventually be paid, but maybe not as much as if they had coded properly, and maybe with a long delay and lots of time wasted by the Billing Dept talking with insurance companies, etc.
In these cases, the coder who knows that there is a (small) error that would make a (big) difference in reimbursement, may not be in a position to get that changed. In my experience, it typically takes about 3 years for someone in a medical office to have built the credibility where they will be listened to about much of anything.
If you have the proper credentials, you are more likely to be listened to, but when you're working with people, one never knows. It doesn't always work that way.
Hopefully Debby will drop by to add more to this discussion.