Ok just figured it out.
I have been able to repreduce this event in many games and with a 100% success rate.
They bug happens when you upgrade a farm on a 100% farm bonus (i havent tried the 300%s because well i dont use them

). For some reason the 100% stacks from the previos building. What i mean is if i upgrade a farm twice on a 100% bonus then it acts like a 300% bonus of the final type. And the worst part is that if you destroy the building well you still have the 300% food bonus but no farm.
A save then load fixes this though. But i dont like having to save the game just ot load it up because i upgrade my farms

I just hope this gets read.