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.
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: This episode takes place over one day. It's Olivia's birthday at the start of the episode, and at night, she gets the card from her stepfather, implying that it's still the same day. Right before Broyles yells at Olivia in the Harvard halls, there is an establishing shot of Harvard where it is nighttime outside, but inside the building, there's sunlight coming through the windows.
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.
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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.
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.
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.
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.
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?