That was a rules interpretation, not a judgment call. Teams may protest a perceived misinterpretation of the rules, but not a judgment call such as Jim Joyce's blown call.
Even so, as I said before, errors are retroactively turned into hits, and hits into errors. That's a judgment call.
Heck, just recently Hack Wilson was given a 161st RBI for his record season, decades after the fact.
The League absolutely can fix this.