Other mistake: In modern time Natalie Vasquez dies in episode 13 and her character is just discontinued. In flashbacks after that episode she's never seen again. She's not even seen at the graduation day of the trainees, but we see her at the Grand Central bombing, which supposedly happened just days after the trainees became agents.
Continuity mistake: A woman asks to use the restroom. While the owner tries to say that it's out of order, a customer who just finished using it returns it. The keyholder is in different position between shots, with the most noticeable difference being the fact that the key is on one end or the opposite in the reverse shot. (00:03:25)
Continuity mistake: Shelby is talking to Caleb with the sack of garbage in between them. Caleb tells her she has a tissue (possibly a "happy" one) stuck to her arm. Behind her, one of the agents is pacing towards the right, to one of his colleagues and past him. In the close-up of Johanna Braddy saying "They shouldn't have let you back in", the man return in frame, repeating the left to right walk that was already well over, and when the close-up is done he is where he was at the end of the previous wider shot. (00:10:50)
Other mistake: The footage from Simon's CCTV cameras that shows Alex hitting him does not match the actual scene; for instance, look at the very last supposed camera shot with Alex pulling the hood up on her head; she uses the wrong arm (left instead of right) and Simon is in a weird position in the middle of the entrance, almost facing the opposite direction and not in a corner like in the original scene. (00:30:10 - 00:34:00)
Continuity mistake: After training, the towel around Alex Parrish's neck changes position a couple times, despite her hands remaining in her jacket pockets.
Continuity mistake: Near the start, Shelby's hair is braided in one shot, not in the next, then is again. (00:03:10 - 00:04:07)
Continuity mistake: When Dr. Susan Langdon and Simon are sitting while she eats a hamburger, she doesn't have a gold wedding band on her finger. As the scene continues and she takes a bite, a wedding band appears on her finger. When the scene ends, once again she doesn't have the gold wedding band on her finger. (00:39:00 - 00:42:00)
Continuity mistake: Simon has a detonator attached with duct tape, then we see his hand with no duct tape, after the commercial then one strand of tape mysteriously reappears. (00:31:50)
Visible crew/equipment: When the trainees breach a door in the hostage scenario a camera and two crew members are visible in the shot. (00:22:00)
Character mistake: The diploma on the wall in Connor's office for the University of Kentucky, "university" is misspelled "universisty".