I'm getting this too. It gives me the negative modifier for studying magic, but it doesn't set the ruler flag for studying that specific school of magic (or at least, it doesn't tell me the flag is set in the requirements for studying magic. I'm the leader in a personal union, and I think this problem started appearing at the same time? Could just be a coincidence. It did work with this ruler earlier in his life, and has worked without issues before him as well.

Once I integrated them I could study again, so it seems that was the problem.

Can confirm this happened to me too, study finished with no event (success or fail) while having a junior partner in a PU. Once it was integrated, could study normally. Playing as Salla Elyn into Cyranvar.