I killed the boss of a level and died during he gets crushed, but the level doesn't count as victory.

Killing the final boss of a level and dying during the death animation counts as a mission loss.

I tossed the final piece to reclaim a facility into the pit just before my final death. I got the notification that I had defeated the guardian... but my death took priority over me completing the ...

It should count as a win if the boss is dead, even if the team is also dead. The goal was to close the rift gate, even if this was done at the cost of our lives, the mission was a sucsess.