The OP posted they made the flight by 3 mins. That tells me they got there after T-15 and although they were connecting could have been Off Loaded from the flight. Thusly even thou there were empty FC seats they might have no longer been on the flight manifest as passengers, so even scanning the BPs wouldnt have produced anything

Very well possible the GA had to add them back to the flight Manually and felt it was best to get the flight Out and add them after the flight departed, rather then hold up teh whole flight and have it depart as Delayed

I would have been Thrilled I made the flight and didnt have to hang around for the next flight, especially if it was a 45 min flight.Instead of Thanking the GA for letting them get on it the OP bashes away for not getting the FC seats. Oh Happy Days