3rd out + missed plate

[mark1481]

Little League 9-12 year olds.
2 outs.
R1 is on second and R2 on first.
B1 hits the ball into the RC gap for extra bases.
R1 scores, as R2 is crossing home, he actually misses home plate. The Plate umpire witnesses R2 missing the plate.
But in the interim, the defense throws out B1 as he slides into third base for the 3rd out.
But I might ad, the out happens before R2 returns and touches home plate.

SHOULD THIS RUN BE ALLOWED...? Timing, Base not legally (touched/occupied) yet by R2, is the ball dead after the 3rd out, thus not allowing the retouch by R2....?

Also, neither of the coaches saw the miss at home, I'm just a parent who happens to have 24 years of experience but now retired from umpiring, who watches for these things from habit, while attending son's games. I have a very good relationship with the League Umpires, they are old school friends of mine from years ago....