Honeypot: A small network that is setup to create the appearance of major network. Architects of this type of network hope that a hacker might be enticed by the falsely generated "network traffic" long enough to trace the intruder's whereabouts. Its name derives from the notion of flies being drawn to honey.
Worm: Malware, or a potentially unwanted program, that replicates without the aid of being attached to another program. Its purpose can be anything from slowing down network traffic, consuming CPU time, disk space and memory, to stealing (or destroying) data.
The IP addresses (452.34.256.193) used to communicate with "Root" are not possible and IRC is typically on port 6667, not 96. These maybe intentional. Using IP addresses and IRC ports that don't exist prevents potential problems and abuse that could arise from inadvertently using legitimate IP addresses and IRC ports, much like how virtually every phone number used in TV and films has a "555" prefix, which is not used for any legitimate phone numbers.
Reese and Scott Powell take a 1 train to Grand Central Station, and the hitman following them gets off an A train. In real life, neither 1 nor A trains go to Grand Central Station. The platform where they get off the train and call Scott's wife is used by an S train (shuttle) that stops only at Times Square and Grand Central. They wouldn’t use it for a getaway since it goes nowhere. From a production standpoint though, it’s the easiest train to shut down for filming.
At the end of the episode when Root contacts Finch, her final text before disconnecting is merely "...Harold"; however, in the previous shot as she is shown typing this word, the keys she presses are completely unrelated.
Before showing Reese and Scott on the train for the first time, there are a few security-camera-style views of a subway platform, implying they got on the train there (though it is not directly shown). However, if the implication was right, it would make no sense, as it is just another platform at the same station where they got off the train later on, Grand Central Station.
In the subway station, Reese leads the hitman into a bathroom. In real life, no bathroom exists in that corridor. The door Reese opens really leads to a storage room, and then the camera cuts to a bathroom in a studio.
Powell's car has the same license plate (EWQ-2147) as Fusco's car in "Ghosts".
The roles of the Asian policeman coming into Matheson's home and the Asian journalist asking Scott Powell questions in front of his yard at the end of the episode were played by the same actor.
"If there is one thing our little venture has proven, Mr. Reese, it's that people are rarely what they seem" (Finch)
"There are no bathrooms on a stake out, Finch" (Reese)
"I haven't been able to unmask the hacker's IP, but here's a vulnerability in the firewall. Yes! Okay... now we're in. So now let's see who's behind the curtain." (Finch)
"Wait, something's wrong. We didn't hack in, we were let in. It's a honeypot! Incredibly sophisticated... they're using a worm to infect any devices connected to our private network, including our phones. They're listening to us right now, destroy your phone. You know how to find me." (Finch)