nautilus-3.20.0-1.fc24.x86_64
gtk3-3.20.2-1.fc24.x86_64

under X11

1. Start a long-running file operation in nautilus, so there's something in the file operations popover
2. Press Ctrl+N to open a new window

I now have a "free-standing" window (with a titlebar and close button) that will move back to underneath the file operations button on the new window when i move it, which shows up a "Unknown" in gnome-shell's window list, and triggers gnome-shell's focus stealing prevention as there's a "Unknown, "null" is ready" notification.

My guess is that the popover is created and popped out before the window has appeared, creating all kinds of confusion.