Imagine you have the city with temple of forgetting. That gives the city -100% research, which basically results in no research in this city.
But if you start to produce research, it gives you 50% resarch, so in total you have 100% (basic) - 100% (temple) + 50%(produce research) = 50% research, which is a kind of weird for me.
But let's go deeper .
Cast spell "set in stone" on the city. Now you have 100% (basic) - 100% (temple) - 100% (spell) = -100% research. And that is actually subtracted from your faction research.
Definately, that is bug, in my opinion.