If you watched the C.B. Buckner debacle the other night (Nats v. Braves), and then saw him botch another call in the field last night, then you understand that even the highly paid MLB umps are fallible. In fact, some of them are just not that good at all.
Every level of baseball you step down from MLB, things get worse. MiLB, college, high school varsity, then HS JV.
So think of your son's situation like this: The guys making the calls are 4 levels down from guys who screw up with regularity and yet are the best that money can buy apparently. Adding to that, in a typical HS game there are only 2 guys out there, so sometimes they just don't see things that well because you can't be at every angle at once.
What that means is, umpire screwups are a part of the game, and there's nothing you can do about that.
Now, if I see an ump copping an attitude, indicating bias for/against a team or any particular player or coach, etc., I think someone should get that guy off the field for future games. Beyond that, you just have to have faith that it all evens out in the end.
Admittedly, it never seems that way!
P.S.
My pet peeve is the HPU who announces at the pregame meeting at the plate what "my strike zone" looks like. No one has a personal strike zone. The powers that be met and developed this thing called a rule book, and it specifies what the strike zone is. The HPU's job is to apply the rules as written, and he is not empowered to substitute his judgment for the rule book.
But I've learned to bite my tongue when someone says that crud.