Give me an example of what A and B are so I can help you connect them. To point at key plot points, it is a little harder.
You can have the sister and friends to try to find information about the missing people; maybe the sister knows someone else that disappeared, who we'll call Andy, and she also know relatives of them. She confronts Andy's mom.
The mom acts a little off; maybe they react strangely, and say, "What?" when the girl mentions that Andy was Christian and frequently went to church. The girl assumes that Andy's mom either doesn't like the church or that Andy was secretly going to church without his mom knowing. Instead, this is actually because a shapeshifter is posing as Andy's mom and, since they aren't human, can't grasp the concept of religion. So the girl has a false lead; she researches into it more, and maybe she finds out that something strange happened at the church a decade ago, or maybe she doesn't find anything.
You have a ton of these tiny hints; sometimes they lead to nothing, and sometimes the girl comes to false conclusions. Once or twice she might get an actual solid trail but after much progress, she gets stuck and can't get past this one detail, like, if it's a kidnapper, then why have these been happening for more than a hundred years? The solution to this detail, of course, is that there's a whole society, but your readers assume it's some kind of a cult that's lived for generations.
In your spying example, as the characters are moving around, you could casually mention something like:
Danny nodded at Frederick. "It could be that."
Frederick grinned. "Just saying, I'm the best." The elevator dinged and opened, and an orange-haired man stepped in.
You have this orange-haired man, and then you add some more instances of the man in this type of thing. Maybe, to hide the fact that it's always an orange-haired man, you instead have him wear a hat, and say 'a man in a baseball cap.'