Continuity mistake: When John goes to meet his friend, his car doesn't have any logo on the front but when he leaves the apartment, it does. (00:26:02 - 00:29:27)
Continuity mistake: After John's tracking device is removed there is blood on the back of his T-shirt. The amount of blood varies from when he gets on the boat until he gets to the underground shelter.
Continuity mistake: In the underground lab, Dr. Su offers to surgically remove the false memories he implanted in John's brain. He drills a half-inch hole in the right side of John's forehead, which leaves the right side of his face covered in flowing blood. John can't stand the pain, breaks free, and he goes on a rampage throughout the underground bunker, killing every UniSol in his path. As he fights his way through the bunker, the bleeding hole in John's head switches from the right side of his forehead to the left side, then back to the right side again. Also, in the last scene (an unspecified amount of time after the bunker brawl), John has no scar on his forehead at all.
