Recently had a 3 night stay at a Marriott property where I checked out around 10:00 pm. I had to do it in person, due to changing the card on the reservation, and couldn't do it on the app after midnight.

Only 2 nights credited... but of course I paid for 3. If I call them will they adjust this, or will they say I checked out before midnight on the last night and hold at 2 nights?

submit the folio to bonvoy and they can see you paid for 3 nights thus the 3rd night should be credited. next time just walk out after doing the card change and don't tell them you are checking out The hotel will check you out the next day as they will see the room vacated and this wouldn't be an issue

During a multi-night stay in Asia (which was booked separately in blocks of 1-night stays) one night was comped by the hotel as the AC did not work at all; this of course screws up my plans for the total night count before the end of the year. Is there any point in asking for that night to be added to my total room nights since I was there that night (as well as before and after that night)? Or would that be a lost cause?

Lost cause. You cannot receive credit for comp nights, as written in the T&C.

Following up. I sent in a picture of my folio through the 'request a missing stay' form. They responded within about 12 hours, cancelled the incorrect credit, and posted the correct credit.

Too bad it didn't just happen automatically, but they did fix it promptly and professionally.

I'm pretty sure I received EQNs + arrival gift points when I had a stay comped (only happened one time). If you have the folio and it shows check in and out date, I would give it a try.

Agreed it is worth a try. May not work out and OP will need a BU plan

It can work if one out of two or more nights was comped, but if I recall the post we're referring to correctly, OP booked each night individually. A folio with $0 in room charges (non-redemption) will not by accepted by the system, there's no way around it (that doesn't break the rules and carry a small risk with it).