Created attachment 102880 [details]
An example of this bug would be Thunderbird with the Lightning extension. When setting a reminder for the events in the calendar, it pops up a reminder window that should have a yellow bell icon and the regular blue Thunderbird icon for the main window. After upgrading from Ubuntu 14.04 to 16.04 and then 16.10 (not sure which upgrade the error appeared), it now shows the same icon for all windows.
*** This bug has been marked as a duplicate of bug 369658 ***