"GameObject is active but a parent is inactive..." Warnings

Hey guys, I've moved my project to Unity 5b20 (from 4.6) and when I open a scene I get hundreds of warnings that I've never seen before:

GameObject is active but a parent is inactive. Active state is now inherited. Change the parenting to get back the old behaviour!

I have no idea what that means. They refer to game objects that are within a group which is itself deactivated. Why in the world would Unity spit hundreds of warnings when loading a scene because I deactivated a gameObject which is not empty?

Is that a known bug? I mean when you deactivate a group of gameObjects it is fairly obvious that its children are going to get hidden/deactivated. I mean that's always been the expected behavior. Why display warnings about that when you load a scene? Is there a new preference setting to get rid of those?