getting the right replacement after pinch running is a tricky one.
it will only go the defensive replacement hierarchy if the conditions for a defensive replacement are met, which means you have to be winning the game, but typically the sim will not pinch run if you are winning, so this doesn't happen often
if the pinch runner also has a third base fielding rating then that's who will play third base, even if its someone with a D-/D- rating you really dont want playing there. if the pinch runner doesn't have a third base rating, then it will put in someone who does have a third base rating, but i'm not exactly sure the logic of how this works.