Probably on your list already, but just to be sure: In my recent playthrough i thrice encountered the problem, that an enemy was pushed into solid stone. A wall or a rock outside. This happens when large units die (the skylla pushes the adjacent mindfragger into a solid surface).
These cannot be seen or hurt by explosives. Running through the wall with demolition-legs "freed" the mindfragger, but the one outside trapped in an inaccessible rock could not be reached. -> Mission failed.
That's a major buzzkill.
Is there a quick work-around to at least safe the missions? Implement that a units that is unable to move 10 turns or so becomes paralyzed (thus captured), or is simply taken out of the victory conditions?