To me it says accounting dropped the ball & didn't get back to Amex in an appropriate timeframe so Amex granted you the credit, not necessarily that they changed your rate at check-in.
But - here's the takeaway IMO - which I've said to others before & do myself. Create a folder for Marriott (or any hotel) reservations & when you receive the confirmation email, put it in the folder. Then you don't have to worry about rate changes, as you have back-up.
The FDC should have been able to see the change history (ie, if a rate was changed & when & by who), but if you had the email confirmation documentation, then there wouldn't be any question. Also, going from memory here but doesn't Marriott show the average when rates change on a reservation, so perhaps you thought you were booking something less than what you actually did (ie, one night was more than another). Since you don't have any documentation, no way of knowing.
Cheers.