I have played all my games the same way till now with a younger to train, and this kind of thing happend for the first time tonight...
You're fairly lucky it hasn't happened before, then. The last few minute substitutions might be based on the trainee's stamina and fatigue, and they're definitely annoying but short of only dressing five players for a match, there's no known way around that. There are also the cases where one of your players is going to the line when the coach decides that it is garbage time, and all the backups come in - including the shooter's backup replacing your trainee because the FT shooter can not go to the bench.
Unfortunately, the standard response from BB is and will continue to be that the game was not designed to guarantee 48 minutes of training in a single game for a single player, and that this therefore is not a bug. We all just have to do our best to work around that since it's not likely to change any time soon!