I had a mission to counter the tactical sense dark event. I sent a squad to infiltrate and the timer ticked down to 1 hour left. At that point, the dark event completed, despite the fact that the mission was still up and it still said successfully completing it would counter the dark event. I did the mission anyway but it did not remove the dark event.
Unfortunately my earliest geoscape save is from many game days ago, so I can't provide a useful save.
Suggested fix:
If possible, add a slight geoscape delay of maybe ~3 hours to the end of a mission to counter the dark event and the actual completion of the dark event.