Sorry to hear about your minutes getting screwed up. This happens a lot. It would be worse if you only needed 30 seconds to get your 48+. I don't train anymore but I will again in the near future. What I always tell trainers is that if you train one position you can only guarantee 2 players getting 48+. And two position training only guarantees 5 trainees 48+. You are always going to be one man short. Out of position substitutions happen when a player is injured or in foul trouble (LCD).
You used SFDC if I read your post right. Did you choose let them play in the foul trouble option? Either case, ill take your word for it since I didn't review the game. Just have to choose who you want to train in a consistent basis.