Stoping clock to set ball

[bwm57]

Gee Ed, thanks for your help.
Actually our team won, I don't have any kids playing in the youth organization anymore, but I'm still helping out on the board.
I was just wondering what was the correct call and thought I would ask someone who knows a lot more than I.
It was first and goal from about the 4 yard line, about 12 seconds left in 4th quarter, running back ran up the middle, his arm and the ball crossed the goal line, then he was burried under a pile of players. The 4 referees were untangling the pile of players and discussing if his knee was down before the ball crossed the goal line, that is when they signaled to stop the clock, they decided he was down before the ball crossed the goal line, spotted the ball about a foot outside the line and wound the clock to start. QB sneaked and scored with 1 second left on the clock, extra point was good for a 1 point victory.
There was a lot of debate if the clock should have been stopped, if it had not been there would not have been time for the last play.