Hi there, I have recently played a game with a custom faction that had Earth magic and the faction penalty to research (-10% research).
Now this didn't bother me really much since I thought my Sovereign would alleviate this by choosing the Scholar Perk to gain another +10% research for a total of 1% loss (or 0%, depending on how you calculate).
But I found first of all that the Scholar perk does not work whatsoever, and secondly I tried using the new spell "Set in Stone" to boost my military cities production through the roof, and crank out some soldiers and new infrastructure. But noticed something very odd about the research.

I Brought you this simple picture to show you specifically that the research generated by the city is NEGATIVE, and if I had essence in all my cities I too would have tested if I could make the research go backwards.
It actually did Deduce these 0.3 from my total amount of research points gained, and was NOT helped back up by scholar (not in the other cities as well).
Hope you get to fix this.
Edit: Forgot to put it in FE Support
Sincerely
~ Kongdej