Technically you cannot "group" Layers. Layers are at the top-most level of the Layers Panel and "Grouping" layers is not possible. You may be referring to "nesting" layers into other layers. Nothing that I know of would cause them to become "un-nested" unless you moved elements around by copy and pasting. Can you provide a screen image of your fully-expanded Layers Panel? This might help clarify what's happening.
Nodes? I'm not familiar with that term in regards to Illustrator. Maybe it's a new "feature" in CC 2017 that I've not heard of. Maybe someone else has an answer for you.
You might be talking about the circle to the right of Layer items. This is an indicator showing whether an item has an "Appearance" assigned to it. Appearances can be moved, deleted or duplicated by dragging these filled circles to other objects, groups or layers (Option+drag to duplicate), or by dragging them to the trash icon.