Visible crew/equipment: When Oliva punches Mitchell Loeb and he collapses against the car, you can briefly see the reflection of some crew members, one wearing a yellow jacket. (00:44:00)
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.
Visible crew/equipment: Right as Ella is downloading the brain-melting computer program, when we see Rachel cooking, it is possible to see crew members reflected in the pot on the stove.
Continuity mistake: Near the end of the episode, when Brian Dempsey is threatening to kill himself, the gun he is pointing at Olivia switches hands. He is holding the revolver under his chin with his right hand in closeups, but in shots of Olivia, he is pointing her gun at her with his left hand.
Visible crew/equipment: When the sellers get out of their vehicle, the reflection of a camera is visible when they open the doors. (00:36:05)
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.
Visible crew/equipment: After Olivia shuts down the bomb, Peter asks, "How did you do that?" and in the wide shot showing Olivia saying, "I don't know," a light from outside the building brightens the room, and you can briefly see the reflection of a crewmember in the glass window. (00:44:15)
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)
Inner Child - S1-E15
Continuity mistake: This is when Olivia goes to visit the boy at the hospital the second time. She and the guy from Department of Social Services go outside to talk. One of the shots is flipped. Note Olivia's notepad and the heart monitor by his bed. (00:19:40)
Inner Child - S1-E15
Continuity mistake: Olivia stops The Artist at a checkpoint, and he touches his face with his hand. When the shot cuts to Olivia, his hand disappears; when the shot cuts back to The Artist, his hand reappears. (00:43:20)
Inner Child - S1-E15
Continuity mistake: When Olivia calls Broyles to ask him to move the child, the shot of Broyles answering the phone is a recycled shot from the episode "Safe". In addition, the shot is flipped, as can be seen by the fact that Broyles' watch is on his right wrist rather than his left.
Audio problem: When Olivia calls Astrid to tell her it wasn't Walter's research, we cut to Astrid who says, "Good news", but her lips do not move. (00:33:57)
Continuity mistake: The blood stain on the door of the Animal Control van changes in size. It's much larger when Olivia runs past it to help Charlie.
Plot hole: When interrogating Boone, Olivia shows him a photo of a body with the spine torn out in the woods. This body hasn't been found yet, as a later scene has Olivia and Peter go to the same location and find the body. You can tell it's the same body because the shirt is the same in both the picture and the crime scene.
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.
Continuity mistake: At the very end of the episode when Nina Sharp exits the elevator, she mostly steps out of the elevator completely before the masked men come and shoot her. However, when they review the security footage of the attack in the next episode, "There's More Than One of Everything," you see that she barely takes a step before being shot. (00:49:15)
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.
Visible crew/equipment: At the very beginning of the episode when Susan Pratt is calling for a taxi, you can briefly see the reflection of a boom microphone on the passing taxi.
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)
A New Day in the Old Town - S2-E1
Other mistake: The killer from another dimension shape shifts into the appearance of the victim, leaving the victim's body. But it transforms into Charlie's appearance and leaves behind its former female nurse shape, hiding Charlie's body to dispose of later. It would have needed to transform from the nurse shape, not out of nothing. The original nurse's body was not at that location.
Suggested correction: The shapeshifter transformed into Charlie using his dead body which it then disposes of at the end of the episode.
But when the shapeshifter transforms into Charlie, he shouldn't be leaving the body of the nurse behind since he had killed the nurse before entering the hospital and transformed there into her. The only dead body in that last scene should be Charlie's.