This is bizzare. The following screenshots are from a MLB quickstart with no settings changes. I am showing the difference between team hitting and pitching stats on the first year (with normal stats) and the second year (where pitching stats become all-around good). This happens on every MLB quickstart in ootp 18 on my mac, and on a test on my PC as well.
Hitting - note how RBI gets much lower despite other stats staying the same:
Pitching - note how both FIP and ERA get lower despite other stats being similar:
It's like clutch hitting suddenly became impossible...