Hey, i have a similar issue but it doesn't get fixed by the workaround.
I'm playing as Schalke and i can't upgrade Youth Junior Coaching at all. Which is pretty frustrating considering I'm playing a youth development focussed save.
If i follow through with @amberhelix workaround, it will always show minimal youth coaching. If i load the safe and check Facilities before checking Affiliates it will always be on Average Junior Coaching.
I have several affiliates, one being my B Team - which has exceptional Junior coaching. And a dutch one in Twente. I'll be trying to remove Twente as soon as possible and see if that changes anything. But as of now, the workaround doesn't work for me