Continuity mistake: After Fauxlivia shoots Joe and is dragging him to the bathroom to dispose of the body, she hears a knock on the door. During this shot, she is dragging him with his jacket over his head, which she is gripping. However in the immediate next shot, she is still dragging him by his jacket, only the jacket is much lower.
Continuity mistake: Right at the very end, Olivia comes to meet Peter at his place for drinks. While Peter goes to grab his coat, her hair moves behind her right shoulder in a consecutive shot.
Continuity mistake: When Walter is using the hammer on the block of ice, the pattern that results is different when viewed from each side.
Character mistake: When Walter is saying his father was a scientific pioneer at the university of Berlin, Peter reacts by saying: "Yeah, I know. Who came here in 1933, which is long before the Nazi's ever took power." In fact it is EXACTLY when the Nazi's took power: 30 January 1933. (00:19:00)
Visible crew/equipment: When Walter and Olivia leave the hospital in the alternate universe, William Bell pulls up in his vehicle. As he does, you can see the reflection of the crew on the metal bars in the front of the vehicle, as well as the metal side-view mirror.
Visible crew/equipment: When Olivia spots John taking off in his SUV, the reflection of a crew member's head is visible when she opens the driver's side door. (01:13:35)
In Which We Meet Mr. Jones - S1-E7
Deliberate mistake: Dunham comments that she works for Homeland Security. While the FBI is under the jurisdiction of the Justice Department, she works as part of a special Homeland Security task force; so saying she works for DHS is an accurate statement.
Continuity mistake: The front license plate on John's SUV falls off during the chase with Olivia. It reappears seconds later. (01:15:30)
Continuity mistake: When Olivia crosses over to the other side you see people wearing FBI jackets. But according to later episodes that had changed to Fringe Division on the other side years earlier.
Brave New World: Part 1 - S4-E21
Continuity mistake: This is when Peter and Olivia are discussing different Boston's suburbs as their potential new home. The sun is on the right side of Olivia's face in one shot. In other shots, it isn't.
A New Day in the Old Town - S2-E1
Visible crew/equipment: Lighting equipment is reflected on Nina's sunglasses when she tells Broyles to "save the day" after the Senate hearing. (00:31:40)
White Tulip - S2-E18
Factual error: Right before the cut to the title credits, the Via Rail Canada logo is visible on a train car, even though it is supposed to be taking place in Boston.
Continuity mistake: At the club, when Peter and Olivia are looking for Valeria, Peter is wearing an ear piece in his left ear. When he talks to the woman, the piece is missing.
Factual error: When they show the fact sheet for Dr. Bishop, his license is marked revoked, yet the license in the picture was not around when Dr. Bishop was locked up. (00:00:15)
Night of Desirable Objects - S2-E2
Continuity mistake: Just before Walter's hand goes numb, Jean the cow can be seen alone in her pen. Then in the next shot, as Peter walks behind his father, Astrid has instantly appeared in the pen with Jean, brushing her. (00:13:40)
Power Hungry - S1-E5
Visible crew/equipment: When they're transporting Joseph Meegar out of the building and into the ambulance, you can see the reflection of the boom mike on the open car door, (the car Charlie is putting Mr. Fischer into). (00:41:00)
Factual error: When Walter removes the glass disk from Bowman's hand, he asks for a forcep, but is given a hemostat, which he uses to pull out the disk. My mother is a doctor, and when she saw this scene, she burst out laughing.
Brave New World: Part 2 - S4-E22
Continuity mistake: The left side of Peter's face is alternately bathed in sunlight or not throughout the scene when he and Walter talk in front of Olivia's hospital room.
Inner Child - S1-E15
Continuity mistake: Olivia, Broyles, Peter and Walter are visiting the boy for the first time at the hospital. A small bit of Olivia's hair is in front of her left shoulder. Cut to the immediate next shot from the patient's room and all of her hair is behind of shoulder. (00:07:05)
Visible crew/equipment: During one of the shots when they corner Mitchell Loeb at the phone booth, you can briefly see a reflection of the entire crew on one of the cars.