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Plot holes
The NSF 'accountant' is labeled 'Terrorist Leader'.
In the "New Dark Ages" ending, Bob Page looks bewildered and asks Helios what's happening. This in spite of the fact that, within the game itself, he was begging JC to not overload the reactor just moments before. This discontinuity is probably due to the ending being pre-rendered before the level design was finalized.
Daedalus states that he found Elizabeth DuClare and she was dead. A newspaper that can be read earlier in the game already states that she is dead.
Several underwater systems do not make sense, with one case in the Hong Kong level having a large vertical pipe full of water while all the other pipes have lower water levels. In the case of water levels, water drains into pipes until all levels are equal.
The name 'Napoleon Bonaparte' is misspelled 'Napolean Bonaparte' in a newspaper article.
Spelling and grammar mistakes in in-game text.
In the antenna shack on Liberty Island, there is a radar screen. There is no radar on Liberty Island, nor any reason that a satellite antenna system be connected to one.
Stepping on grass gives off the sound of stepping on gravel.
Activating environmental objects such as machinery doesn't draw attention from hostile NPCs.
At the 'Ton Hotel, a room door has to be unlocked from the inside.
The Player is given the option of disabling cameras. This action should obviously attract the attention of anyone monitoring the camera feed.
In the supposedly 'free' clinic in New York City, services only seem to be available for money.
After going to Hong Kong, there are still unconscious bodies left behind in New York City from previous missions.
The NSF 'accountant' is labeled 'Terrorist Leader'.
After analyzing the Gray Death's molecular composition, Tracer Tong mentions that the viral structure is made up of multiples of 17 and 23. He then adds, "1723... the birthdate of Adam Weishaupt [founder of Bavarian Illuminati]." Weishaupt was in fact born in 1748.
The U.N.A.T.C.O. chief states that the Player killed N.S.F. personnel on the Lebedev mission even if he didn't.