Am I missing something here?

[JJ]

In Illinois I'd fill out a SAWA report - it's a special incident report that can be filled out online or in hard copy - and explain what happened. It gets sent to the Illinois High School Association, and the baseball guy there will contact the umpire and the school(s) involved and explain the correct ruling.
There is no formal "protest" in Illinois, but this is a way to make sure that same ruling does not happen again by that umpire crew as well as letting the schools involved know that there was a misapplication of a rule.

JJ