When Armin approaches Annie in an alley to ask her to help Eren escape, Annie agrees but puts on her ring (with the blade). Armin later realizes that she knew from that moment that he was lying. How?
There were also no people on the entire route Annie notices and even says it. Also, Armin and co wanted Annie to come with them underground where they would subdue her. If Mikasa wasn't there she would have done it no problem because she knows she would beat Eren and Armin. She might know that titan shifters can't transform with no sunlight, as seen when even tried to turn into a titan in the well but couldn't. With Mikasa there, hand to hand combat is iffy for her but take away her trump card and add Eren? She wasn't having it and called their bluff and was able to see through the lie.