This is a workaround:

First install this package:

sudo apt-get install compizconfig-settings-manager

then opening the tool, general options > display settings and setting
overlapping output handling to either prefer smaller monitor or prefer
larger monitor (depending on which resolution the external monitor has).
In my case the external monitor has 1920x1080 whereas the laptop has
only 1680x1050.

The "smart" mode that is default isn't so smart after all I guess..

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https://bugs.launchpad.net/bugs/1181197

Title:
  Adding a secondary screen causes both desktop icons and all active
  windows to move to it

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