The most egregious example has to be the major events with Lin and Felicity during 0.18--both events end with the character in question away from the hotel. Then click, you're back at the hotel, and there she is; you and the other characters can interact with her as though nothing had happened (and that ignores the fact that the entire premise for Felicity's event is false--the "dirt" they'd found just isn't there). But then at the next events for these characters, they're presumably going to be back wherever you left them.
These are explicitly a compromise solution to the problem of episodic releases - once the game progresses far enough, they'll both return to the hotel in the natural course of events, and you'll be able to continue grinding their non-story scenes, and progress other characters' storylines through scenes that involve them. With the updates only progressing the individual stories partway through those characters' absences, if there was no way to interact with them until they returned, you'd soft-lock a bunch of stuff until v0.22 or v0.37 or whenever the absences ended.
Having the characters pretend to be around while they're absent, until an update brings them back, means players can't soft-lock themselves, without forcing it through making them complete absolutely everything else before being able to play the disappearance events (and even that has potential issues if the disappearance lasts several updates).
So, yeah, Felicity and Lin being kinda around for the purpose of avoiding soft-locking other storylines until some future update is something I'm very okay with.