It looks like you have the first two scenes working just fine. Scene 1 shows a red cube, scene 2 shows green. I'm not sure what your plan is but you have 12 copies of the green cube on Layer 2.
[image: Zm3e_Screenshot-3_20_201911_22_23AM.png]
You've also managed to assign edges and faces of the green cubes to layer 2 instead of Layer 0 where they belong.
I've fixed the layers problem, removed 11 of the green cubes leaving just one, made a copy of the cube, painted its faces blue and assigned it to Layer 3 and now it all works just fine.
Scene 1
[image: iHXT_Screenshot-3_20_201911_32_16AM.png]
Scene 2
[image: 5fv5_Screenshot-3_20_201911_32_26AM.png]
Scene 3
[image: TuQy_Screenshot-3_20_201911_32_36AM.png]
If you want to place copies of the same group in the exact same position but on different layers, try it this way.
Original group created on Layer 0.
Create the number of layers you need and name them appropriately. Turn off their visibility.
Select the group.
Hit Ctrl+X to cut it to the clipboard.
Hit Edit>Paste in place. A keyboard shortcut is a good idea for this.
Immediately change its layer association to the first layer. It'll disappear because that layer's visibility is turned off.
Hit Edit>Paste in place again. A new copy of the cube will appear.
Assign the next layer in the list to it.
Rinse and repeat until you have copies of the component on each of the desired layers.
Set up your first scene with the first layer visibility turned on but all the rest turned off.
Create the scene.
Turn off the first layer, turn on the second.
Create the next scene.
Repeat until you have all of the scenes created.
