brumey1107:

As a novice umpire, can you explain why in OBR and NCAA the PU put the ball in play illegally?

Your other two questions were answer but this one wasn't.
The PU can't legally put the ball in play unless the pitcher is on the rubber with the ball. If F3 has the ball then the PU did it incorectly. It's no big deal, just return the ball to the mound and start over again.