I agree about the UFOs, but for terror sites, it's a different matter. For example in XCF, your job is to fight and destroy various cults and other sinister organizations, usually culminating in storming their HQ. It feels weird if you just completely destroyed their structure two weeks ago and they still go about their business as normal, because it's still the same month.
I realize my example is not super strong, since you can explain it away with "there are still uncovered cells which carried the operation" etc., and often you'd be right. But at other times not really, when the enemy in question for whatever reason functions more like the droid army from the prequel trilogy of Star Wars - once you kill the brain, you kill the entire network.
So while it's a limitation I can work around, or write around, sometimes it's not that easy and may feel forced to the player.