there can be two major reasons for your trainee being subbed out.the first one being that you play too many players in the scrimmage and your trainee has low stamina.so when he tires off the coach subs him out.
secondly if you are playing decent amount of players but you use let coach decide then he is bound to be subbed out.
so u should try not to play more than 9 players in the scrimmage(better keep it down to 7) and place your trainee as the starter,backup and the reserve of the position where you are plying him and use strictly follow depth chart