Why Not Pinch Run?

Down one in 9th with slow footed runner on second of 1-9. Several on the bench better than that with the best being 1-15. There was a defensive replacement option for the catcher that should have been removed from second. There was no pinch hitting being done to hold back the should have been used pinch runner. Of course game ended with the runner on second being thrown out at the plate. The player on second was not mark dont pinch run for.

Any ideas...?

Sad thing to make matters worse I carry three catcher for the reason to be able to pinch run for. Even thou that opens up the possibility of the top two catchers being hurt at the same time. Which is exactly what happened in the very next game. The top two catchers got hurt in the same game.