Everybody plays a different game (league) and may not play the same way so it is impossible to match our observations to yours. Can you quantify what you see? Is it every game? How many runs? Do you have too many PB and WP per AB league wide? This you can check in-game. Go to stats/team stats and on the pitching and defense tabs you can see league total output. Check those numbers vs total AB and then you can compare to whatever type of league you have IRL.
For runs to score somebody has to be on 3B most if not all of the time. Do you have too many triples? Maybe not enough DP so too many guys make it to 3B.
Sorry to be long winded. More info needed.