This happens also to me often with various applications, but not only
when focused from dock, also when a window automatically loads in
foreground, but focus remains on the previous one seen.

Some examples and screenshots :

I run a program, ie Firefox, in a maximized window, triangle in the
right side of Unity dock, which indicates the focused application, is
well put on Firefox icon.

If, just before switching to Firefox, I've run Update Manager or
Synaptic to download some packages, manually switched to Firefox, at the
time downloads (or update verification) are finished and packages begin
to install (or if there is a partial update available), Synaptic (or
Update Manager) comes himself in foreground (without I click on its
icon).

But the right triangle remains on Firefox icon. So, a click on Firefox
icon to go back on Firefox does not do anything, as default behavior in
Unity, when an application is selected, is that click on its icon does
nothing.

So I have to manually click somewhere in the Synaptic window (to focus
Synaptic) or to an icon other than Firefox to select this program, and
again click to Firefox icon to come back to Firefox !

Other problem, global menu is the one from Firefox, and if I click on
the left"X" icon to close Synaptic, it's Firefox which closes as it is
focused...

Another example :

Same thing if I have Firefox reduced, Gwibber maximized. If I click on a
link in a tweet, Firefox reappears automatically maximized in
foreground, but triangle on Unity dock remains on Gwibber, same problems
of selecting / focusing / global menu / closing...

** Attachment added: "Unity-Focus-FF-UM.png"
   
https://bugs.launchpad.net/unity/+bug/813714/+attachment/2236335/+files/Unity-Focus-FF-UM.png

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https://bugs.launchpad.net/bugs/813714

Title:
  Unity places the wrong window to the foreground when focused from dock

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