don't know about the cause but this bug is still affecting me.

e.g. unity-mail

1. Install unity-mail
it depends on: gir1.2-gnomekeyring-1.0, gir1.2-gtk-3.0, gir1.2-indicate-0.7, 
gir1.2-notify-0.7, gir1.2-unity-5.0, python3,python3-gi, (xdg-utils), 
(indicator-messages)
in brackets what was already installed
2. check in history that even the other packages were installed
3. remove unity-mail
4. check in history that just unity-mail has been removed
5. apt-get autoremove doesn't find anything
6. you just have to remove the dependencies by hand
7. note that no other packages is affected during removal (nothing else depends 
on those packages)

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https://bugs.launchpad.net/bugs/467539

Title:
  software center does not remove auto installed dependencies

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