Revealing mistake: Episode 15, "Faceoff": When the agent fires the hook to get to the roof of the church, it does not reach the balcony. However in a following shot you can see the agent climbing there. (00:10:05)
Continuity mistake: Episode 15, "FaceOff": Sophia gives Elias one hour to get the buses or else she will destroy Washington. When this happens, the sun is high, and by the time the buses arrive it is already very dark outside. (00:03:05 - 00:34:15)