Quick update: I called Marriott, and talked with a great agent. They were able to get the points back into my account. It's annoying that I still have to be nervous about cancelling a reservation or SNAs online, because I'm not sure if they will get automatically credited back to my account.

"It's a glitch" isn't very comforting, when the reservation is for hundreds of thousands of points. The website certainly knows how to deduct points accurately every time.

It's the Marriott equivalent of having to call Delta multiple times to get a RUC correctly applied to a flight.