If there is a group node at the location where you paste elements, the pasted elements will automatically be assigned to that group node.
Now, if you use CTRL+V for pasting, yEd chooses the paste location close to the original (copy) location. If there happens to be a group node at the chosen location, the pasted elements end up being assigned to that group node. If you do not want that to happen, then you need to tell yEd where to paste the elements. This is done by opening yEd's context menu on empty space and choosing "Paste" from the context menu.