In the scene where the forensics team is going over Nancy Lewis' apartment when Olivia is walking towards Peter to help him cut the glass she's wearing blue gloves. When she holds the glass she uses her bare hands.
Susan Pratt's driver's license shows she lives at 955 E. 61st St. However, when she leaves her building, the number over the door reads 530.
There is a jump cut during the first self-immolation scene. The nearest spectators are shown being flung back from the blast, but then it cuts to a brief moment before she explodes. It is possible this edit was related to the so called dueling timeline theory.
Susan Pratt has a work ID from the New York Highway Dept which does not exist. Toll collection in the state of New York would be operated by either the NYDOT or the The New York State Thruway Authority. It's possible this was done for safety concerns.
At the beginning when Walter is showing Peter and Olivia the comparison of the typewriter and the Manifesto, the "y"'s are not the same style.
At 25:05 the two, nearer, buildings adjacent to the United States Capitol, the nearest of which is red brick, do not exist. Nina is walking past a building that is not in the vicinity of the U.S. Capitol.
Olivia is outside an office located in Charlestown when she sees The Prudential Center, 111 Huntington Avenue, and The Keystone Building. However, none of these buildings are visible from Charlestown. The position of The Prudential Center and 111 Huntington Avenue would put Olivia's location somewhere near the Christian Science Center or Berkley College of Music. In addition, The Keystone building is nowhere near either The Prudential Center or 111 Huntington Avenue.
Walter has reportedly read the manuscript a dozen times and has circled a series of uses of the letter "Y". However, the page he shows Peter contains several other visible words containing the letter "Y" that he hasn't circled.