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.
Continuity mistake: During one of the first shots of Olivia in the tank, you can see the reflections of lab lights on the water even though the tank is closed.
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: Olivia is pretending to be Raoul's friend at the bar where his brother works. When talking to the guy, her hair moves back and forth in front of her right shoulder throughout the whole scene.
The Arrival - S1-E4
Visible crew/equipment: When John Mosley, the stocking-capped man exits his car, you can briefly see the camera's reflection in the glass window behind him. (00:13:30)
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: 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.
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)
Other mistake: In the scene where Peter and Lincoln are driving to question Daniel Hicks, a crew member is playing a practical joke that was somehow missed in editing. If you look at the left side of Lincoln's face, someone is hitting him with a laser pointer. This is definitely not part of the script (i.e. Sniper rifle scope), as no one is actively targeting members of Fringe in this part of the show. (00:16:20)
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: At the beginning of the episode, when Christopher is putting Loraine in the car, her stomach changes from bulging outward to flat and normal in one shot.
Continuity mistake: When Olivia says "Freshman", Peter and Walter are seen screw driving wires into Roy's head. In the next shot, the wires are gone and they are drilling in his head. Later on, they use the screwdrivers again. (00:36:30)
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 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: When the sellers get out of their vehicle, the reflection of a camera is visible when they open the doors. (00:36:05)
Other mistake: Peter and Dunham are alone in an apartment with blood coming in under the door. They are called and leave for the subway. Peter should have had to walk through blood to leave.
Factual error: An aerial view of the "Miami Tower" (in Miami, Florida, of course) is labeled as "Boston Federal Building".
6:02 AM EST - S3-E20
Continuity mistake: This is after Olivia has bumped into Walter in the hallway. She gets back into bed and tells Peter that his father is walking around the house naked. Peter laughs and says it's normal for a Tuesday. The sun is on Peter's left cheek in shots from behind Olivia. In the reverse shots from behind him, the sun is missing. (00:07:30)
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 Charlie looks up the file on David Esterbrook, he says that the file shows that Esterbrook is directly responsible for INtREPUS' "controversial" R&D, including pre-natal gene therapy, human/animal hybridization, and viral warfare. Yet later, Olivia says she can find no dirt on Esterbrook who is, in her words, "cleaner than snow". If INtREPUS kept records of their illegal endeavours, then how come Olivia can't find them when the time calls for it?
Answer: He helped his father evade capture, impeding the investigation.