They did it in *Pine tar gate*.
It would hurt no one to have changed it and righted a significant mistake.
The pine tar incident did not involve a decision based on judgment; it was a decison based on the application of a rule for which no judgment by the ump was required.
On the flip side . . . there is no avenue under which a team can formally protest what is simply a bad call by the umpire -- even a blatantly bad call. And even if there was, there is no point in re-playing anything if the ultimate outcome of the game wasn't affected by the call.
In the pine-tar game, the Commissioner’s ruling was that the umpire erred in interpreting the rules when he called Brett out for having used a bat with pine tar that was too high up (on the label), and the home run should thus be reinstated (but the bat confiscated and not being eligible to be used in a game again). The blown call last night was not an error in rule interpretation, but an error in a judgment call (safe or out), which is an entirely different thing. Judgment calls need to be made (and corrected, if other umps had a better view) at the game by the umpires, not by the Commissioner.