In the flash back to when the resonator was deployed, Baird hangs back and watches the resonator briefly before Marcus tells him to hurry up. When the player actually witnesses this scene, Baird immediately joins the others after setting up the resonator.
In the wine cellar, when Sergeant Fenix tells Jack to rip the door into the secret laboratory, he puts his hand to his ear as if he is using the communicator to summon Jack. Jack had previously been summoned by characters simply speaking.
Weapons don't actually just switch hands when changing hands; they flip, with even bolts being on the other side.
Characters occasionally reply to other characters before the other characters have finished speaking.
Fuel tanks are shown being used by way of being set on fire by Stranded. It is not possible for them to be used in this way because the valve prevents fuel from exiting anywhere but the valve.
The threads on the drilling platform elevators go the same way regardless of the direction of travel.
The repairs that Baird said he would need to do to get the APC running require a repair facility and much more time than Baird has.
In spite of having a cloaking device, Jack doesn't hide in many of the fire-fights.
Sergeant Fenix tells Dom that he could get into a lot of trouble for getting him out of prison, and Dom says otherwise, but later Dom contradicts himself, saying that he could get into a 'lotta shit' if Command found out that he was there.