A few more steps:

I could reproduce the bug with firefox, Software center and with absolutely any 
application I tried, under a certain condition, and it's interesting.
Try this: 
- launch firefox and do absolutely nothing with the window.
- open nautilus : no bug, it works.
- Close nautilus, back to firefox.
- Click any dummy place on the firefox window
- Open nautilus: here is the bug. Now
- close nautilus again, back to firefox.
- The focus is on the window but don't click anywhere.
- Open nautilus: no bug, it works fine.
You can repeat it as many time you want I guess with any application. 
Therefore, it looks like windows can either just have the focus, and then 
nautilus can get it too; or  they can clutch at their focus if you've started 
clicking, interacting with them (not with their menus though), and then normal 
applications can grab the focus from each other anyway, but nautilus can't – 
maybe because it has a special role, being a process that is always running in 
the background and hence starting it only brings up a window but does not 
actually starts anything. In other words, it looks like there are two sorts of 
“having the focus” in Unity, and nautilus is not adapted to it. But it's only 
an intuition... As for the LibreOffice windows, they seem to directly pass on 
to the 2nd “clutching focus” without the need to interact with them.
Hope this will help !

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https://bugs.launchpad.net/bugs/994949

Title:
  When nautilus opens it is not the active window

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