@Alex K. There are many issues like this, where trust, credibility and fairness come into play.
Our company management contract has a list of what rental income will be applied to and in what priority. This is also programmed into our PM software, so it happens automatically.
Our lease also states what rent will be applied and in what order and also a security deposit.
So, you may want to check these documents to see if this is covered with your PMC.
While we always try to be fair with our clients, we also have to generate enough income to pay our bills.
In your case, you mentioned your PMC tried to collect the final rent payment. How were they compensated for their time spent on this? Typically, it would be covered by the late fee income.
Perhaps you could discuss this with them and they may decide to adjust the charge. They are within their rights though to deny your request.
In a perfect world, PMCs would be able to track exactly how much time their staff spent working for an owner and then charge based upon those hours & an hourly rate.
Pretty sure most owners would end up paying more if this was could be done.