Looks like something broke in the code... This thing never happened to me, and statistically, it should have - with many enemies unconscious after end of all missions, multiplied by 100 or 200 missions...
I think something like this has only happened about 3 or so times and only once where it went about 6 six turns out of 500 or so capture heavy missions, but many of those missions didn't have non surrendering units in them IIRC. Also that was with the older OXCE and Piratez versions mentioned in a previous post in this thread.
Edit: pressed post instead of preview
This story is a combination of 2 old bugs and 1 new bug.... I'll be looking into it...
Congrats on finding the new bug. This one sounds tricky, but hopefully finding it was 3/4ths of the battle.