During the "Terminus" level, when Sanchez knocks out 47, the red tie 47 always wears is intact. When 47 comes to, the tie is completely missing from his outfit, yet when he makes it outside the hotel, the tie has miraculously reappeared.
Diana is shown to have red hair and green eyes in "A Personal Contract" while the file ICA has on her show her hair is dark and her eyes are listed as brown.
At the end of the level "A Personal Contract", 47 can be seen turning to point a gun at Victoria, the back of his head shows that he is wearing a band-aid. The scene where 47 cuts his bar code happens much later in the game.
When Agent 47 ends the journey on Birdie's bus prior to going to the Orphanage, he has bird feces on his head despite there are no birds in the bus.
In Mission 18, a resident of Blackwater Park is denied access to a building. He then talks to another man, saying that he had called 2 different people who could let him and his wife stay over, only he never is seen calling anyone.
Spelling errors in the subtitles.
When Agent 47 gets a text message on his cellphone, the screen says 'incomming' instead of 'incoming'.
The "prostate cancer guy" incorrectly uses the voice of a Dexter Industries guard. This is due to this interaction originally being in the "Dexter Industries" level.
In the Terminus level when 47 shoots the maid in the private area, she is moving while she's killed.