Dark events applying before mission timer ends

[Aetherlift]

Is it meant to be the case that dark events begin before the mission to counteract them ends? I've been having them start applying when there's still like a day left to do the mission, and then doing the mission doesn't actually stop the dark event. I dunno if its intentional or not? If its intentional it seems really counter-intuitive to have the mission countdown timer just be totally misleading, and I'd try to change that if possible?