First time for me

[JerzeeRef]

I have not had a chance to hit the books regarding this play from earlier today.
17u, following FED rules. R1 on third base, 0 outs, 3-0 count on batter. Next pitch in the dirt (ball 4) off the catchers chest, ball rolls to his left and comes to a complete stop. R1 breaks for home, catcher gets ball throws wildly past the pitcher who is covering, into the first base dugout. Batter runner slowly walking up the line watching the play behind him. I call time from the field, as the ball rolls into the dugout. Partner at the plate never saw the ball go into the dugout. As I hustle over to my partner (batter runner is now at first) I tell him I'm 99.9% sure that we place the runner at third due to the base on ball award (1st base) and then a ball (not a pitch) being thrown into dead ball area. Partner was 100% positive, that we had a first play from the infield, so the 2 base award would be from the time of the pitch. Him being the plate and senior man, we agreed to place batter runner at second base. Neither coach said boo, all was quite, but I kept thinking did we kick it ?