While the pilot is flying around, the Player can find a seaplane that wasn't there before.
While fishing, during reeling in a fish, when the fish jumps above water, the reeling stops, and starts again once the fish is back in the water. While this is likely for animation purposes, the reeling should actually speed up given that the fish is no longer in the water.
The Player watches a broadcast from Seed even though he is not near a television set.
A trailer is shown with its lights on, even though no truck is hooked up to it.
NPCs who use flame-throwers do not have a hose connecting the flame-throwers with the tanks on their backs.
Even after cultists have been killed at a location, they may be there again if a mission is set to that location.
Some of the guns eject on the wrong side.
In the 'Hours of Darkness' expansion, the Player is able to communicate with a firebase. The Americans didn't have the ability to do this without backpack-mounted radios.
Metric units are used in the 'Hours of Darkness' expansion; the metric system was only in limited use by the U.S.A. during the Viet Nam War.
Measurements are given in metric. The U.S.A. mainly uses Imperial measurements.
Plants are shown growing in a cave wherein sunlight can't reach.
In the opening scene in the church, Rook puts handcuffs on the Father. He still wears these as he boards the helicopter. After crashing, Father no longer wears the cuffs and no explanation is given as to how he got rid of them.
Resistance members are shown burning a pick-up truck at the garage - for no reason.
In the missile silo, the Player is tasked with destroying computer equipment to free prisoners. Destroying equipment can't make it perform a task.
After liberating the hotel, a cutscene shows a Resistance member knocking boards off of windows. Given that this is to become a base, it makes much more sense to leave the boards on.
The jail is never strengthened with mounted machine guns despite it being turned into a base.
Even illusions are attacked by allies.