Actually went through the same thing for a stretch last season. My trainees couldnt get 48 minutes, blowout or not, unless I played 5 guys. Trainees usually played 46-47 minutes. Even when I played with 5 guys in a few games my trainee fouled out or got injured. In one scrimmage played 6, trainee also got subbed in the end.
Posted it as well and there was no clear consensus on the reason. This season so far am now able to get 48 minutes. Only changes are: my trainees are older, have higher stamina and different teammates.
IMHO its a combination of stamina, players on the court, the opposition, and chosen tactics - the GE fielding the most "logical" (based on its algorithm) lineup at the moment but I have no concrete data to back it up.
What I did last season was just focus on 2 trainees. Not ideal but what can you do? <shrugs>