How should (could) this have been handled?

[SamG]

Sitch:

Bottom of 5 (only play 5 inn.). Tie game. 2 outs. R1 @ 2nd, R2 @ 1st. B5 hits a line shot to center field. While the fielders are chasing the ball, R1 goes home (scoring the winning run) and to the dugout. Home team celebrates, visitors are dejected, but gather their stuff and go home.

As things are being cleaned up, as PU comes off the field he tells visitor parents & coach that the winning run never touched home plate. Neither parents nor coach complained, just accepted it.

Forgetting for the moment a) PU shouldn't have said anything and b) game is over, not worth appealing (it was a Middle School 'B' game), how could/should this have been handled from the defensive side? This is assuming someone on defense (coach, player, parent who informs coach) noticed the player didn't touch home.

The player was in the dugout by the time the ball got back to the pitcher. So, I'm assuming the DC appeals to the PU that the runner never touched home? Can the catcher do that? Since the runner is in the dugout, that's an out, right? 3rd out, game still tied, start extra innings?

I'm trying to find out what should have been done so *I* (if I end up coaching again) or my daughter would know what to do if this happens again.

Thanks