It's frustrating to no end, and if it makes you feel any better, there are usually 5 threads a week from managers having the same problem as you. I suspect you did everything right with the tactics setup, but it's just one of the frustrating hiccups in the game that does this. The only foolproof way to guarantee your trainee gets 48 minutes is to only put 5 guys in the lineup and hope he doesn't foul out.