I've some problem moving nodes to layers.

For any object, I understand that there's the Shape node and the Transformation node.

When I click-select an object on the scene and put it on the layer, I'm effectively putting that Transformation node onto the layer.

The problem comes when some of the Shape nodes are on different layers.

E.g.
Let's say I have two layers, layer 1 and 2.
I click-select an object, let's say an Apple, and add it to layer 1.

Somehow, somewhere, let's assume that someone added the Apple's Shape node to layer 2.

Now if I were to check the visibility of both layers, I'll be able to turn the visibility of the Apple off. This is not what I want.

Question: Is there a way to click-select an object, add all it's nodes, Transformation and Shape, to a layer?