Larry Watson

High school game tonight. 1 out bases loaded. Fly ball to left field for an out. The runner from third tags and crosses the plate. The Runner from second leaves early. Throw comes into the cutoff man then goes directly to second base where the second baseman touches second and the runner leaving second is called out. The inning is over but umpires allow the run to count. Is this correct? My argument was if the runner that started on second base was tagged on the appeal the run counts but because the ball went to second and the out was recorded there the run should not have counted