Goof (errors in geography): Despite being set in Boston many of the neighborhoods bear no resemblance to the actual Boston neighborhoods they are supposed to represent.
Goof (errors in geography): Beginning in season one, establishing shots show the teams headquarters to be in a skyscraper which title cards identify as the "Boston Federal Building." However the building shown is actually Hancock Tower, a privately owned office building which is one of the most recognizable landmarks in Boston. The FBI is located in One Center Plaza which is across the street from Homeland Security office located in the John F. Kennedy Federal Building located downtown at Government Center. Both buildings are in direct proximity to Boston City Hall, a city courthouse, police station, local NBC/CW television station and immigration offices.
Goof (errors in geography): All shots of "Harvard" are actually Yale Univ. Mostly cross campus courtyard and Old campus courtyard.
Goof (errors in geography): Agent Dunham calls from South Boston and says that Agent Scott is "headed South on Fenway." The Fenway is nowhere near South Boston.
Goof (continuity error): In the car chase between Dunham and Scott snow appears and disappears between shots.
Goof (factual errors): Charlie makes reference to a tip from "Back Bay PD." The Back Bay is a Boston neighborhood but does not have its own police force and is nowhere near Chelsea, where the tip directed them to.
Goof (errors in geography): The pilot is supposed to be set in Boston yet the geography is clearly not that of Boston and every shot which shows the skyline is clearly that of another city.
Goof (revealing mistake): When Peter is speaking to the two Iraqi men regarding the pipeline, after stating that he speaks Farsi, the shot of the two men ceasing their conversation and shifting in their seats is obviously the previous shot of them beginning their conversation, except reverse frame order.
Goof (continuity error): When Peter gets up to go to the interrogation room to speak with Dr. Steig, the video display in the background shows Peter stepping in to the room before he gets anywhere near it.
Goof (continuity error): SPOILER: When John is dying after crawling out of his overturned car, several snippets of movement are repeated as well as his arms/hand changing position and his eyes being closed on one angle yet open on the next.
Goof (continuity error): When Agents Dunham and Scott go to the storage unit, it is snowing heavily and the ground is covered in a layer of snow. However, when Agent Scott is inside the storage unit, there is no snow on the ground outside and it is raining.
Goof (continuity error): When Olivia chases John along the highways both the amount of snow falling from the sky as well as the amount on the ground changes from shot to shot.
Goof (factual errors): The FBI is under the Department of Justice, not Homeland Security.
Goof (factual errors): When they show Iraq for the first time, it's shown that two Iraqi guys speak Farsi to each other (with a very weird accent) and they American guy tells them "I also know Farsi". That's while Farsi is the language spoken in Iran, not Iraq. In Iraq they speak Arabic.
Goof (revealing mistake): The German spoken by the passengers and crew of the airplane in the beginning is sometimes grammatically incorrect, sometimes nonsensical, and often tinted with a heavy American accent.
Goof (continuity error): During the final car chase the vehicle headlights are alternately on and off.
Goof (errors made by characters, possibly deliberate errors by the filmmakers): While attempting to lull himself to sleep at the end of the episode, Walter recites a sequence of numbers which is known as the Fibonacci series, where each number in the sequence is equal to the sum of the two preceding numbers: 0, 1, 1, 2, 3, 5, 8,13, 21, 34, 55, etc. The problem is, he skips 5.
Goof (plot holes): When Walter and Olivia are going through the files they find a connection to a Dr. Penrose. Olivia motions for Farnsworth to run a check on him. Farnsworth types in a search for "Dr. Claus Penrose". Neither Olivia or Walter had mentioned his first name though.
Goof (errors made by characters, possibly deliberate errors by the filmmakers): Astrid mispronounces Dighton "Ditton." It is correctly pronounced "Die-ton."
Goof (errors in geography): Stoughton, Massachusetts is completely landlocked and as such has no bridges. It is also several miles away from Sudbury, Massachusetts.
Goof (factual errors): A computer readout for a DEA employee reads "Drug Enforcement Agency" when in fact "DEA" stands for "Drug Enforcement Administration".
Goof (errors in geography): One scene supposedly takes place at Boston College, but the establishing shot shows a building which is of a different architectural style from Boston College and the neighborhood which Olivia is shown driving through looks nothing like the neighborhoods around Boston College.
Goof (errors in geography): The final confrontation is supposed to take place at South Station, which is a real transit hub in Boston. However, the building shown is considerably smaller and different in architectural style from South Station.
Goof (continuity error): The positions of the "frozen" bus passengers change between the shot of the police officer discovering them and the subsequent scene of the main characters investigating the scene. Most obviously, the dead DEA agent disappears from her frozen position between the two scenes.
Goof (audio/visual unsynchronized): When Walter is showing the puzzle pictures in the lab, he does so with a video projector, which is obvious from the rapid changing of the highlighted demonstration slides of the rabbit/duck image without a phase of black in between them; the sound however the machine makes each time Astrid clicks on the remote is the one of an old slide projector, mixed with a rather uncommon beeping sound.
Goof (factual errors): At Agent Scott's funeral, the flag is shown draped with union over the right upper corner of the casket, but it should be over the left front, or the heart.
Goof (anachronisms): In several photos depicting events that supposedly occurred in 1987, A US Marine is shown wearing the US Army's Army Combat Uniform (ACU), which was not fielded until 2005, and the Advanced Combat Helmet (ACH) which was not fielded until 2002.
Goof (anachronisms): Agent Dunham asks Col. Jacobsen about 1987 at Quantico. When Jacobsen shows her a picture of Master Sgt. Stewart Malik, he is obviously wearing digital camouflage utilities which were not adopted by the Marine Corps until 2003.
Goof (anachronisms): At one point we are told a story of a Marine at Quantico in 1987. When we see him pictured, his equipment is modern and his uniform / camouflage is recognizable as the ACU. This uniform is used by the Army, not the Marines, and was issued in 2005.
Goof (anachronisms): When Agent Dunham is shown the photograph from the 1987 Quantico incident, the Marine is wearing ACUs, which weren't issued until after 2001.