Zig Zagged: At first, it appears that they are brother and sister, but then it comes out that they are merely faking it. Then they both get paternity tests and discover that their parents are the same, but then it turns out that her parents are clones of his ...
Alice and Bob act exactly how a brother and sister would act in real life.
Alternatively, Alice and Bob aren't related, the relationship is exactly as planned and no squick is involved.
The writers make a deliberate decision to mess with the fans' minds.
Alice was hastily changed from a love interest to a sister.
Lampshaded: Charlie: "Yeah, and you're totally not paired with Alice." Bob: "I'm not!"
Writer: "OK, I admit, Alice and Bob's relationship took turns I never intended."
Deconstructed: Since the author fails at writing Alice and Bob as siblings, the fans think that they are a really cute couple. So, the author tweaks the storyline and ends up with much better work than their original plan.
Reconstructed: Still, the author feels that the early chapters were not his or her best.
Plotted A Good Waste:
A case of Blatant Lies; the writers know exactly what they're doing with Alice and Bob, but the series will be over before they'll admit.
The story is a Mind Screw, so the trope needs to be played for true mindfuckiness.