You can assign your 3 leftover players to spots you do not want to get 48 minutes in. The ones you want to get to 48 minute mark must have one player in all spots (starter, sub, reserve).
I agree, the coach AI is not perfect. I don't know when will the AI be revised but I'll try to remember and point out this lapse in order to get it fixed. Sorry I can't be of any more help.