Holman's sunglasses are knocked off when he is pistol-whipped by Lian, yet he is wearing them again when the game resumes and he's lying unconscious on the floor.
Ramirez's face changes from the generic "GI" model, in the early Colorado levels to a more unique model in the later Agency Bio-Lab level.
At the end of the game Mara Aramov, speaking with Vince Hadden, says that as the Secretary of State he will become president when the administration falls. This is factually erroneous as if the President and Vice President were to depart from office the Presidency would pass to the Speaker of the House of Representatives. Developers realized this and, when repeating the scene at the beginning of Syphon Filter 3 change the line from "become president" to "have the power."
In Mission 19: "New York Slums", the M16 assault rifle's firing sound-effect is inexplicably changed to the one for the HK-5 sub-machine gun.
Some friendly NPCs can be seen wearing t-shirts even in cold weather.
Morgan shoots the pilot at McKenzie Air Force Base with a silenced 9mm pistol, yet the gun emits a loud bang instead of the quiet pop a silenced weapon should make
Missions 19: "New York City Slums" and 21: "Sykes Parking Garage" are set in the Lower East Side of Manhattan. The Twin Towers of the World Trade Center should be easily visible in the skyline, but they do not appear.
The Agency takes CDBC agent Dobson captive from Kazakhstan to Colorado for no reason, other than to be killed by Dr. Weissinger via lethal injection.