An error, either by the GA boarding the flight or the system and this has the potential to happen.
I’ll never forget an instance I had on DL. Flying CVG-ATL-MSY. we got to to ATL fine, though delayed due to storms and our flight to MSY was delayed a couple of hours until ~midnight. At boarding, literally a couple of dozen of us can’t board due to the scanner beeping, so GA sent us all to gate desk to get sorted. He was also desperately trying to close the flight as fast as he could. GA at desk realizes what’s going on, and basically tells us all to get onboard and take any empty seats and they will sort out later. I realize this was going to cause problems…biggest concern at the time was records of something happened on the flight.
anyhow, unsurprisingly when I am able to actually get through to DL reservations (which took a day or so…storms in ATL don’t treat people trying to call in well, but that’s well know with AC anyway😀

, they can’t see our flight for the return. They were able to reinstate it, but I suspect many others on our inbound had some issues trying to check in to their returns as well.