This is a situation where it kinda depends.
If you have a package, you have to have it paid in full by a certian date. So you would not normally run into this situation.
If you have a room only ressie, which it sounds like you did in this case, you have to pay at check in.
With that said, being that you arrived past midnight, I can see where your card was charged ahead of time. (Ive had this happen to me at times at other hotels.) However, they should have been able to reverse the charge when you handed them cash. Or so I would think.
For OLCI, you have to put a card down for incidentals. When you pick up your room key, they want to zero out your account. That means charging your card if using OLCI since the whole purpose of OLCI is to avoid having to really do anything or interact with anyone. You would either have to pay the balance before you arrive or bypass the OLCI experience.
But to be honest, I dont think OLCI saves a lot of time in the long run, so if you dont do it, I dont think you will miss much. Just pay your balance upon check in.
PS... This also brings up the idea of debit vs credit cards for checking in - OLCI or the "traditonal" way. People need to remember that Disney will put a hold on debit cards for certain amounts. (Value=$500, moderate=$1000, Deluxe/DVC=$1500.) That hold takes a while to get released. Better to use a credit card at check in and pay the balance in cash, debit card, or other means at the end of your trip.
Just mentioning this since I know that some people would like to not use credit cards for their vacation expenses.
Hope that helps....
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