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.
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)
Stescalade - S2-E3
Other mistake: Lydia's phone is upside down when she calls Lucas. (04:50:00)
