outfielder puts up two hands

[BEAREF]

Watching a game last night where the center fielder put up his hands because the ball when under the fence. The umpires did not stop play by calling time and the baserunners kept running until all three had touched home. At that point the base ump went to verify whether or not the ball had indeed gone under the fence and then they placed the runners on the bases...2nd and third and one run scored. Is this the correct procedure? What would you do if the ball had not gone under the fence?