I can confirm this error on Linux Lite 3.0 (Ubuntu 16.04 base):

jerry@jerry-vb-32:~$ software-properties-gtk 
/usr/lib/python3/dist-packages/softwareproperties/gtk/SoftwarePropertiesGtk.py:40:
 PyGIWarning: Gdk was imported without specifying a version first. Use 
gi.require_version('Gdk', '3.0') before import to ensure that the right version 
gets loaded.
  from gi.repository import GObject, Gdk, Gtk, Gio, GLib
/usr/lib/python3/dist-packages/softwareproperties/gtk/SoftwarePropertiesGtk.py:40:
 PyGIWarning: Gtk was imported without specifying a version first. Use 
gi.require_version('Gtk', '3.0') before import to ensure that the right version 
gets loaded.
  from gi.repository import GObject, Gdk, Gtk, Gio, GLib
Gtk-Message: GtkDialog mapped without a transient parent. This is discouraged.
jerry@jerry-vb-32:~$

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https://bugs.launchpad.net/bugs/1576193

Title:
  software-properties-gtk complains about Gdk being imported without a
  version

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