How do you correct this problem?

[umpire george]

Girls fast pitch, 18U
1 out, R1 on 3rd base, R2 on 2nd. Batter hits liner toward F4 which hits ground inches in front of her glove. Both runners try to advance and F4 throws ball to plate. R1 scores and things settle down, for the moment.
Plate umpire states ball was caught in the air and batter is out. Defensive coach tells F2 to get ball back to 3rd base because R1 left on release, appeals her for leaving before ball was caught.
Big problem is plate umpire did not loudly and quicky yell out on catch.
Base umpire, R1 and R2 had good angle on hit and know ball hits ground before being caught. That's why both runners attempted to advance.
Time is called by base umpire to try to straighten things out.
What is the correct thing to do to make things right?