I colonized 2 planets, same turn, and chose malevolent both times.  When I picked up the first malevolent ideology tech all 20 points were deducted from my total.  When I went back and colonize, chose, colonized, I was able to get 2 ideologies and had 20 points left over.

  Steps to reproduce:

   Have 2 colony ships ready to colonize 2 planets at game start (buy 1).  Save game.  (I have one if you need it)

   A)  Colonize both planets, choose same ideology decision both times.  Pick up an ideology.  All 20 points should be deducted, leaving you with zero.

     Colonize 1, pick an ideology.  Colonize the second, pick second ideology.  You should have 2 ideologies and still have 20 ideology points left to spend.