it has to be something from left field. Someone didn't turn in recommendations or endorsements or he got torpedoed by someone he trusted. Or something was entered into the system wrong or miscalculated.
That is the only possible explanation short of an angel descending and commanding them to reject your son because he has another path God wants him to take.
Think about it. BYU is not more selective than Harvard or Yale. The narrative you present is impossible. So there is something else you don't know about.
I would tell your second son to not worry about it one bit. HIS stats are shoo-in stats and he should just keep on keepin' on.
I hope you do eventually find out what happened and when you do, please post it here so that we can all understand.