CPU will sub guys in prior to the game if someone is below about 30% energy whether you have lineups on AUTO or MANUAL. The issue with this is that they will completely redo the lineup, rather than just subbing out the tired guy. Meaning they will leave in the well rested guys but they will completely change the batting order if they sub even 1 guy.
The only way to combat this to check the CPU lineup in the pre game lineup menu. If I see anyone below 30% energy I will back out of the game and go into the lineup screen in the franchise menu. I will take out anyone in the lineup that I know the CPU will be taking out due to needing rest. I will also put guys at DH who have about 50% energy to make sure they play all 3 games in a series.
One thing I do recommend is saving your franchise before you start every game. Sometimes the CPU will sub guys out for a reason besides rest. For example, Player X is only hitting .125 vs lefties this year, or Player Y on the bench hasn’t played in over a week and the CPU wants them to get them playing time. The cool thing about this feature is that it is NOT pre coded into the game. Meaning it doesn’t happen every time you play the same game. Therefore if you saved the franchise prior, you can close the app and reload the franchise. I can almost guarantee the CPU will not pull said player for performance issues this time around.