Happend to me a couple of months ago on ATL-SAT. My inbound was supposed to be late but catched up lots of time and we had no issues with that gate. I rushed over and boarded with my AF-issued BP. I was upgraded T-7 so seat was 3A. The machine beeped, showed my name and seat number (as encoded in the 2D barcode) - all good. However, my seat was already occupied. The GA who investigated confirmed that I was moved to a later flight.