To clear it up:
With the "auto-end battle" option enabled, if you eliminate the last remaining enemy on your turn and you have any wounded units, you're given the chance to not instantly terminate the mission so as to take care of the wounded. If the same thing happens on the enemy turn (or, though extremely unlikely, on the civilian turn), the mission ends right there and then, so you never get to treat your units. A common scenario is the last enemy firing and wounding your units and getting reaction killed. How about making it so the mission termination is delayed in such cases?