I don't think there's a solution. I used to be crazy unlucky with wonky subs (likely due to blow outs) and would complain so much. I can't vouch with certainty that I've tried this, but I'm pretty sure I'd tried everything in the past and settled on trainee/trainee/trainee at starter/backup/reserve.
Just try avoiding blow outs, maybe match your trainee on a player with a lower FT rate, and maybe avoid zone defences. May help, may not.