Do you have the same problem when opening other files, for example pictures? If you do, it might be that you have set Nautilus to be always on top. "Always on top" is set in the menu that opens when you click the window's title bar with secondary mouse button. See this image for menu reference (Gnome on left):
https://spin.atomicobject.com/wp-content/uploads/always-on-top-gnome-kde.png. It is my understanding that the setting doesn't persist if the window is closed, so you can test this just by closing and re-opening Nautilus.