In Priority assignments where decisions are made after the first two missions in the chain, the decisions are broken.  

For instance, when choosing to  let the heretics get a ship to avoid collateral damage, or to fight them on the ground because assisting them is heretical; I chose to fight them on the ground, but the text said that it was easy to get them ships, and that I now will board their ship.

In another priority assignment, I had discovered that the cultists were working with xenos.  The choice was to get them to turn against each other, or "two birds with one bolt round."  I chose to purge them both, but the dialogue said it was "pure gold" watching them turn on each other.  I also believe that i lost the morality that i gained earlier in that assignment.