There's no excuse for the rude behavior, but the problem with your theory is that if the mistake was on the part of the GAs, it seems they would have gone out of their way to rebook and make him happy. It sounds like it was an actual glitch** and the GAs were confident nothing could be traced back to them if/when the inevitable complaint is filed.

Maybe your relative had zero interest in 2.5 hours in Y, but I'm not sure I would've missed my flight over this, especially with the long resulting layover.

(** I recall similar reports here recently of people being checked in on the app but then being told they weren't checked in at the gate. It does appear to be a possibility, as odd as it seems.)