I had that happen years ago... Late inbound. Sprinted across airport. Got to the gate when they were in the middle of Boarding - about T-25m. Ticket would not go through... agent simply said 'we didn't think you would make it and we were not going to hold the plane for you, so we marked you as a misconnect'. Had to argue like crazy to get biz seat back. (i.e. I am here, you are in the middle of boarding!) Finally relented and got a seat. (There were several others from my connecting flight that showed up just before boarding fully closed. I did not see any of them on the flight.) So yes, it does happen.