Likely the agent isn't looking at the reservation. They're looking simply at the ticket, it says OPEN, and concluding you didn't fly. Nowadays miles post based off the ticket. Thus they likely don't know hpw/aren't trained to look at reservations system. I'm betting it shows you onboard. For whatever reason (IRROP, computer hiccup, etc) the flight coupon for that flight segment remained OPEN instead of closing.
if you hadn't boarded, the reservation (not the ticket) would have auto canceled all remaining segments.
Was there IRROP/SDC/SDS/something out of ordinary that happened?