When Dr. Joe Harris is carrying Maura through the tunnel, he sets her down, where she then cuts him with a sharp object. Where did she get this from? The scene before, when she was being knocked out with the rag again, she didn't have anything in her hands.
Maura leaves a clue about tunnels, but she had never been in the tunnels nor could she have any idea the kidnapper was going to take her into a tunnel.
At approx. 39 minutes, Joe Harris has just knocked Maura out again, and the camera is on her. Just then, a female-sounding cough is heard, but off camera.
Angela tells Maura's biological mother, Hope, that Maura has been abducted, but not her adoptive parents.
When Maura asks Joe Harris why he used her to provoke Jane, she wonders why he did not use Jane's sisters instead. But the only siblings of Jane that have been mentioned so far in the show is 2 brothers.