I can only imagine the chaos behind the curtain a few hours before a flight departure. People checking-in, changing seats, families wanting to sit together. Automated systems protecting people that have misconnected, humans rebooking people that have misconnected, SDC, Op-Ups, Airport Upgrades, etc. etc. etc. There are likely dozens of people and automated systems all with their fingers in the same pie....across multiple airlines with independent systems...all this on a framework with parts of the system designed 50 years ago.
I'm actually impressed at how well it all works and that there are so few glitches like this that occur.