If you have traveled the world then you know that hotels can't just modify their front desk billing system to suit your individual requests.
The resort fee is added to the folio for each room nightly. There is no hotel folio system or workflow to move only the resort fees to your room's folio. You could have prepaid all the resort fees for all the rooms at check-in. This would have been reflected on each folio as a room credit. As an alternative you could have stopped by the front desk on night before checkout and paid the resort fees for each room to clear the folios for check-out processing early on the check-out day.
I worked for a major hotel chain for a while (not Marriott or Disney). You are absolutely correct about the logistics of how the resort fees should work; however, the resort should have explained these options to OP. No one should assume OP knows this, and the front desk shouldn't just be saying "yes" to appease the guest when that's not logistically possible.
you have to ask for it if you expect anything.
I respectfully disagree. Good customer service will offer something as a goodwill gesture without the guest having to ask for it, particularly when its an issue through no fault of the guest such as the double charges or room maintenance issue. Part of me thinks that perhaps the resort is tightening their reins in light of the increased operational expense this year, and perhaps that's why nothing was offered. If that's not the case, then someone at the hotel dropped the ball from a service perspective.
Did they actually charge your credit card or just put a credit authorization your card?
Either way, it puts a hold against their available funds and will take a couple of days to either be refunded or for the hold to fall off, so its kind of a moot point.
You're having an event for six rooms worth of people in the middle of a pandemic. I think you should have expected things to go wrong. I'm surprised they even let you do that.
Why should they expect things to go wrong? The resort has been open since the summer, which is ample time to adjust to their "new normal". And they are operating at a reduced capacity, which means there's less guest volume to contend with. Besides, the issues described by the OP are nothing that relates to changes as a result of the pandemic. These issues could have happened at any time for a myriad of reasons.
why does a credit not do the same?
When you make a charge, you see the funds held against your available balance as an authorization - not a charge. The merchant's swipe/insert authorizes the card for the amount you're attempting to charge to validate you have the available funds on your card to cover the purchase. The charge typically then posts to your balance within 1-5 business days, depending on the speed of your bank. Similarly, when you receive a credit/refund, the bank will process the request from the merchant within 1-5 business days (on average), depending on the speed of your bank. Every bank will have different processing times depending on the volume of customers, how sophisticated their internal systems are, etc. Bank processing, both for credits and debits, occurs through a nightly batch process that happens on business days only - its not instantaneous.