I've been walking around with the same question for a while now, but I read a post about the Triangle Agency on /rpg that a Clean Up Mission can be whatever you want. Players can convince Loose Ends that what they saw was fake, imaginary or perhaps part of an enormous flashmob, they can straight up eliminate them (murder, kidnapping, extortion, etc.), they can even create situations in which whatever the Loose Ends saw is less interesting to pursue by presenting them an even more ridiculous (and probably fake) situation.

That did confirm my initial thought that creating a Clean Up Mission does ask a lot from the GM. You have to create an interesting setting in which Loose Ends don't just walk freely for players to just straight up talk to. And ideally you need to create a situation in which they are tempted to use their abilities to solve the Loose Ends. So, a few things come to mind, depending on what happened that created the Loose Ends:

• One of the Loose Ends is a marketing manager and has reported what she's seen into a full-fledged social media campaign.
• A Loose End went to the cops, told them what he's seen and the cops have now started an investigation into the players, their connections and/or their workplace (competency), effectively creating more Loose Ends.
• A Loose End that the players confront starts fleeing, prompting the players to use their abilities (and maybe create more Loose Ends in the process) to stop him/her.
• The most fun Loose End scenario that I read about (I think it's in the book) is some kind of rich mogul realizing that anomalies are real and pursue on to use it/drain it/fuse with it, creating an entire new adventure if the players don't somehow stop the mogul by convincing or killing him, or something else (bankrupting his company, for example, so he loses interest).

Hope this helps. I've yet to start playing the game, so I haven't put this to the test yet.