What you have to look at is the pitching rule. You have #5 as the Pitcher of Record. #25 comes is as a substitute and bats for #5. #5 re-enters for #25. Number #25 never pitches to anybody so he can not be a pitcher during this game. With #5 on-base, the coach can now enter a courtesy runner, number #13 for #5. As stated the courtesy runner is for the position, not the person. You have to decide did they violate the pitching rule, they did not violate the courtesy runner rule. When you dis-allowed them that option, you screwed the pooch.