Couple of things come to mind, but not sure since you mention bench coach and not manager are you both GM and manager? Or are you GM and hired a manger for you MLB club?
1.If you have an AI MLB manger they can retain some decisions for themselves even if you have put yourself in control. Unless you are in "legacy mode".
Game Settings>Global Settings>
GM only users are always in control of lineups and hiring (legacy mode)
The checkbox for this mode is at the bottom of the left panel of the Global Settings page.
2. You have a fatigued player and the AI redoes the lineup to put in a sub and give the starter a day off.
This one could get you if you are simulating a few days at a time. The AI does this to me, but I play out all of my games so will catch the change in the pregame screen allowing me to "fix" it in whatever way I think is necessary. My guess is this is not your issue as I think you would have already spotted it. But figured better to throw it out there just in case.
If you are in "legacy mode" and it is not due to fatigue, I'm sorry, but I don't have an answer.