I've had this happen at Hilton, ICHG, and probably most often at Marriott. I have even gotten the first response, "you arrived after midnight so you don't get credit" on a few occasions. But they have always eventually fixed it.

I have never explicitly pointed out the scenario upon check-out and asked them to back-date or otherwise rectify the check-in record, but that seems like a good tip that might prevent some of these occurrences.