Per Marriott, it was because it started as a 3N reservation (2 FNA and 1 on pts) and I changed the reservation to 2N. The crazy thing is, they 3rd cert was taken weeks after the reservation and I easily could have missed it since there's no way to see redeemed certs. It took about seven hours on the phone to get an agent who themselves could find where it went, they got my cert back and comp'd me for the headache, but then Marriott took the comp back. Raised it with Lurkers and eventually a Case Resolution Specialist got back to me, said they "spent a considerable amount of time" researching it, claimed I misrepresented what happened, and threatened my certificate. Thing is, per whoever did the actual investigation, it's exactly as I said, though they never commented on the rep (great) support from the rep who initially reissued and comp'd me.

This is the quote from guest services: "When the stay was modified the 50,000 Points were returned. Somehow at some point after the guests stay their [certificate] was attached to the booking as well which should not have happened."