Question for the experts!

[Redraider]

I coached a 10U game tonight and the following happened: (and I'm sorry it's not in the official umpire lingo!)

2 outs, bases loaded, batter hits to pitcher who throws it to 1st base. 1st baseman drops the throw, but picks it up and the batter is out. In the meantime, the runner on third scores. The team at bat claims that the run scores, because the initial play to first was not clean.

Our umpire was a kid and he had no idea what the ruling was. It was no big deal, because it wasn't a close game and it was in the last inning. But, I'm just curious if the run counts or not.

Hope I explained this clearly. Thank you!!