well, it is not really a bug, it is intended that way. You get the gildar bonus and unlock the harbor and watermill improvements if you researched the tech, this is the benefit. You can argue that the benefit is not enough and should also increase the food production, sure.

There are actually quite a lot of cases where the "+x ->+x" indicators show no increase (harbor -> watermill on gildar bonus for example), it's just there to remind you that the building in the tree you are upgrading from already increased this value.