Are there some limitations with the lights and their includedOnlyMeshes property? I made a test to light the instance (sphere) with point light using includedOnlyMeshes after two seconds and nothing happens. See: https://playground.babylonjs.com/#1FUKMR#4
If the original sphere is used, everything works… 
Edit:
Digged into some code and found this:
Could someone explain what this means in laymans terms? If I have an instanced mesh, the lighting of it cannot be changed? 