This might be a general Rhino thing.
When intersecting two surfaces, the resulting curve is created on the active layer.
When turning a polysurface into a SubD, it is created on the same layer as the polysurface. When the SubD is in flat mode or has creases all the way around, you end up with two identically looking objects on top of each other having to click and select the right one.
It would be more efficient, if there was an option to create the new geometry on the active layer.