Um, move them in z-space? They're 3D layers, y'know.....
AS Dave says, seperate them in Z space so they don't overlap.
If that's not possible, create a 2D solid between each 3D layer, then push the solid(s) out of frame so they are not visible. This will make the 3D layers exist in their own 3D "worlds".
The problem you're describing is normal behavior. If you intersect 3D layers they intersect. Maybe I don't know what you're trying to achieve because you haven't given enough information. A quick screenshot added to your post usint eh little camera icon at the top of the reply form is all we need.