This has happened to me twice in the last couple of days. I believe they were both Anu Haven Defense Missions. Basically I was unable to finish the mission, even after killing all known enemies. Both times they were attacking the power facility of the haven and both times there was a Pandoran stuck in the solid base of the generator. I don’t think they moved there, but where spawned there at the start. I had to resort to the console to end the mission successfully.
For the record, the 1st instance was submitted by F12.
Actually, the generator base is hollow. I had a Scylla destroy the surrounding platform and a Siren found her way underneath. I followed and found her walking there with her head deep in the concrete block above. I submitted a report and shot her dead.
This explains that spooky mission I had one time on one of those very maps where I literally couldn’t find a single enemy.
Another Anu haven defense with enemy embedded in solid matter. This time it was a mindfragger embedded in a pillar of the building. Explosives couldn’t make a dent. Therefore the mission could not be ended. I assume it was hatched there by the Scylla.