What is the basis of the year end bonus, is it fixed, or tied to productivity or such.
If fixed, I would expect all employees would share equally including non clinical employees, so I would expect she would get a year end bonus. Yes, she asked for it early, probably cleaner than floating a loan.
If based on productivity it could be argued that being more productive gives her more work but her bonus would have more tenuous status. But the fact is she HAS been getting them and sort of expects them. The fact that she asked for it early could be understood other than the amount is thus variable so what was it based on.
I suspect there was a mix up on the term stipend and bonus. She gets a monthly stipend which she was calling a bonus for advance. This again may be easier to advance rather than giving her a loan, but needs to be followed.
Stuff comes up. There are creative ways of supporting your employees who I think we will all agree do not make a lot of money. Loans, vs vacation advances vs advance bonus or stipend are all legitimate but you should be aware of what's going on. It may be reasonable to review the entire structure with your PC and set guidelines that you thought were understood just to be on the same page. It might also be reasonable to have the accountant make sure that there were no unexpected transfers that neither you nor the PC were aware of because they may only be looking to make sure the books balance.
Ultimately it sounds like it may have been an acceptable advance but you were not notified. But it also made you more aware of what you don't know and probably should have been aware.