The following strange play happened in a CIF high school game. Important to note these are very inexperienced players, still learning baseball basics. With two out, R1 is on 3B and R2 is on 2B. B1 hits a single. R1 scores and R2 slides safe into home. For some unknown reason, R1 who was already in the first base dugout, seems to think he did not touch home (he actually did), so he runs from the dugout, around the catcher and umpire, and along the third base line and almost all the way back to 3B. Everyone on the field is confused, but the defense tags out R1 who is caught between 3B and home. Home plate umpire signals out, but does so because he doesn't realize that R1 was the first kid to score on the base hit -- umpire assumes R1 was a different player entirely and must have started the play as a runner on 1B and was tagged out trying to advance from 3B to home. Defense runs off the field.
Manager explains that R1 already crossed the plate and was in the dugout already, and that R1 coming back on to the field was simply him not understanding baseball. Here's how the umpire called it (which I know is wrong): R2 is safe at home and his run counts. R1 is considered tagged out and is the third out of the inning. Keep in mind no appeal was ever made. The defense tagged out R1 and ran off the field, assuming that was the third out of the inning.
How should this have been handled? I don't think a runner can be tagged out once he's in the dugout (even if he returns to the field)? And even if the defense believes R1 never touched home, they can't really appeal it because they all ran off the field thinking that was the third out.