Ever since Nautilus had that little thing in the top bar indicating how long it would take to copy or delete something, Nautilus has always behaved strangely, normally showing "Preparing" for the entirety of the time and then magically disappearing when it is done and flashing the icon several times. But the most strange thing of all just happened, and is still affecting me.

I moved a very large folder with many sub-folders and file into Trash, Nautilus reports the following for the properties of the folder "203,334 items, totalling 1.7 GB". So once I had done this I clicked the button to "Empty" the Trash, normally with large items such as this one and the new Nautilus system of indication it takes a while and doesn't appear to do much. But this time it right out failed, it just won't let me delete the folder, though when I copied other things into the Trash as well as this folder it deleted them, just left this folder seemingly.
And then this happened, the indicator became a separate window, and when I closed it, so did Nautilus. But this is what it looked like:

    https://bugs.launchpad.net/ubuntu/+source/nautilus/+bug/1610200/+attachment/4714791/+files/Nautilus_Strange_Deleting_Window.png
    https://bugs.launchpad.net/ubuntu/+source/nautilus/+bug/1610200/+attachment/4714793/+files/Nautilus_Strange_Deleting_Window_In_AO.png

This is the strangest thing so far that has happened with this, and yes, when clicking the close, minimize, and maximize buttons on this new "window", they did do what they do on any window.

This really is bizarre for it to become a separate window. I looked in my syslog and these were the Nautilus logs for that time period:

Aug 5 11:40:05 Cat-Bus org.gnome.Nautilus[3525]: Initializing nautilus-dropbox 2015.10.28
Aug 5 11:40:05 Cat-Bus org.gnome.Nautilus[3525]: (nautilus:12634): Gtk-WARNING **: Theme parsing error: <broken file>:1:0: Failed to import: The resource at '/org/gnome/libgd/tagged-entry/default.css' does not exist
Aug 5 11:47:24 Cat-Bus org.gnome.Nautilus[3525]: (nautilus:12634): Gtk-CRITICAL **: gtk_window_realize: assertion '!_gtk_widget_get_realized (widget)' failed
Aug 5 11:50:07 Cat-Bus org.gnome.Nautilus[3525]: (nautilus:12634): Gdk-WARNING **: nautilus: Fatal IO error 11 (Resource temporarily unavailable) on X server :1.
Aug 5 11:51:16 Cat-Bus org.gnome.Nautilus[3525]: Initializing nautilus-dropbox 2015.10.28
Aug 5 11:51:20 Cat-Bus org.gnome.Nautilus[3525]: (nautilus:13023): Gtk-WARNING **: Theme parsing error: <broken file>:1:0: Failed to import: The resource at '/org/gnome/libgd/tagged-entry/default.css' does not exist

And I still haven't been able to delete the folder. I am running Ubuntu GNOME 16.04 with GNOME 3.20.

I initially filed a report on this issue here: https://bugs.launchpad.net/ubuntu/+source/nautilus/+bug/1610200 But thought I should also do so upstream.