I have observed this behavior in Ubuntu Mate 15.04 and 15.10. Can someone tell me if it is by design or if I need to file a bug?
In a nutshell… When the software updater detects that there are updates available it presents a button on the Window List of the lower panel. However, there is no window visible on the screen. If I click on the button I see a flash of animation - usually seen when a window is minimized to the Window List button. When I click on the button a second time the software update window appears on the screen.
Is this the intended mode of operation? Perhaps the idea being that software updates should not be too intrusive? I can understand the software updater being launched as a minimized window. However, I would sort of expect that clicking on the button once should bring it on screen. That makes me tend to think it might be a bug.
I hate to bother the developers about something trivial - especially if this is “normal” behavior. Any insight?
it may be that you have a slighty broken install instead of it being a bug?. Try running the following 2 terminal commands (Ctrl + Alt + t) and see if anything updates, restart if anything does!:
sudo apt-get --fix-missing install
The above command downloads and installs any missing packages on your system.
sudo apt-get --fix-broken install
The above command downloads and installs any broken dependencies on your system.
So, get ready to change the advice you give 
