During Mission 2, a virus is referred to as an organism. It is still debated whether or not a virus is even alive.
In Mission 3 the Royal Moroccan Army is shown using STRYKER armoured vehicles. The Royal Moroccan Army does not have STRYKER armoured vehicles.
General Zaydan has Chinese PLA ribbons on his uniform.
Everybody in every country speaks fluent English with North American accents.
In a DLC mission, the word 'canister' is spelled 'cannister'.
In Mission 6, the readings of the EKG attached to the heart transplant doesn't match the actions of the transplant.
Agent 47 does not change his accent when disguising himself.
In the stalls used by spice peddlers in Marrakesh, the spice is stocked in such a way as to defy gravity.
In the Mission 3 briefing, a news video of Morocco is shown. The cars are shown driving on the left-hand side. Vehicles in Morocco drive on the right-hand side.
During Mission 3, red-winged blackbirds can be heard. These birds can only be found in the Americas.
Agent 47 can shoot cameras in order to avoid the attention of security; if this were done in a real-world scenario, the operator or operators of the cameras would be alerted that something was amiss.