I had a New Jericho haven called Shianxang in North America. Very early in the game, I uncovered a nearby haven that wanted cybernetics plans, and so “Cybernetics for a Cybernetic Deity” dropped on this haven. I was very close to getting 50% alignment with New Jericho, so I didn’t want to risk it. I essentially decided to forego completing the mission.
When it came time to build Tobias West’s super fortress, this was also the haven chosen to build it. I did not realize that a story-critical mission would drop when this completed. I also did not know that a mission trying to drop on a haven already having a mission would cause the new one to fail to drop and disappear into the ether.
When the popup arrived saying that the Pandorans were attacking the new super fortress en masse, and New Jericho required my assistance, the mission involved with this failed to appear anywhere. I strongly suspect that it is because the haven it was supposed to appear on already had a special mission, and the game couldn’t handle that fact. Either its a bug in general with one special mission spawning on top of another one, or maybe just a bug specifically involving one of these two missions.
Luckily, I was close to getting the Synedrion mist-repellers final option, and I went with that. It wasn’t the biggest inconvenience, but if someone was near 100% on the index, and had no other options near them, I can see it being very frustrating.