I have recently uploaded a save to the SI Cloud Service that this issue was reported with; however, my in-game manager has since moved clubs. I was noticing the issue with Real Betis in LaLiga. The save is larger as I have more leagues and nations loaded. Not sure how to link it here?
In the save, I am now at Southampton, where my U21 and U19s are playing matches. I moved because it was not engaging to have my reserve sides not playing.