I suggest you to read again the Basic physic tutorial especially the note about manual movement & other behaviors.
Pinning two physic objects to each other (knowing that they'll automaticly push out from each other) is to be considered as irrealistic behavior.
You should rather consider making a distance or revolute joint (Advanced physic tutorial).
With such sensible/experimental (the plugin is still to be considered beta) topic as physics I recommand to read both tutorials and the future manual entry (not written at the date of this post, but it should be a matter of days/weeks at this point) often to refresh one memory.