Fixed in upstream commit:

commit 8d15294552b1b47888f16222db2cf1c17482faee
Author: Richard Hughes <rich...@hughsie.com>
Date:   Mon Sep 12 16:50:58 2016 +0100

    Only show the external installed notification on success

diff --git a/src/gs-page.c b/src/gs-page.c
index 852b7e3..8cce6e5 100644
--- a/src/gs-page.c
+++ b/src/gs-page.c
@@ -172,7 +172,7 @@ gs_page_app_installed_cb (GObject *source,
        }
 
        /* only show this if the window is not active */
-       if (gs_app_get_state (helper->app) != AS_APP_STATE_QUEUED_FOR_INSTALL &&
+       if (gs_app_is_installed (helper->app) &&
            !gs_shell_is_active (priv->shell))
                gs_app_notify_installed (helper->app);


** Also affects: gnome-software (Ubuntu Yakkety)
   Importance: Medium
       Status: Triaged

** Also affects: gnome-software (Ubuntu Xenial)
   Importance: Undecided
       Status: New

** Changed in: gnome-software (Ubuntu Xenial)
       Status: New => Triaged

** Changed in: gnome-software (Ubuntu Xenial)
   Importance: Undecided => Low

** Changed in: gnome-software (Ubuntu Yakkety)
   Importance: Medium => Low

** Changed in: gnome-software (Ubuntu Yakkety)
       Status: Triaged => Fix Committed

** Changed in: gnome-software (Ubuntu Yakkety)
     Assignee: (unassigned) => Robert Ancell (robert-ancell)

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Desktop Bugs, which is subscribed to gnome-software in Ubuntu.
https://bugs.launchpad.net/bugs/1568935

Title:
  notify-send shows "application has been installed" even when
  authenticate window is cancelled

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