Hi,
Any Changes on a prefab in the project window will affect to every same prefab object in the scene
A prefab works like that.
so if you would want certain prefabs without the fsm and some with, you should make 2 prefabs.
One with and one without.
Also i think you use the Get Mouse Button Down action?
if so, this action will trigger anywhere on the screen, not only on the object.
The transitions on the image below will work on the object, so you can use mouse down to use on your object :