Ah, so that's why UFO crashes aren't automissionable..
I found a peculiar inconsistency with regards to whether I got any items or not from the missions. Seemingly at random, usually I would get x/y items, sometimes 0/0 items.
Also, in release 2.3, automissions would either succeed with no dead soldiers, or fail with no dead soldiers (it looked like simply the mission dialogue disappeared, but at the top of the screen it would say 'battle lost'). Supposedly this would be based on a score with a random element, so if the score was good enough you had a chance to win, and if you won you would lose no soldiers, and if the score was poor you had to try again.
The problem for me was that more and more into the game automissions would fail, so I would have to retry and retry 4-5 times. This *could* have been due to my soldiers getting crappier - but I upgraded them with nano armor, the latest weapons and all. I would guess the scoring is somehow off so that either the alien score increases too quickly by far (or it increases forever whilst yours are capped by equipment which tapers off) or your score increases too slowly.