Continuity mistake: When Castor Troy (as Sean Archer) says, "Every time you'll look in the mirror, you'll see my face," he proceeds to cut his face. The first cut he makes is straight down the side of his right cheek (viewer's left) and later that cut is curved and closer to his nose. This may appear to be a mistake at first glance; however, Castor's facial expression is different in the two images. When he made the cut, the cheeks were pulled away from the nose; in the second photo, the muscles are relaxed, moving the cut closer to the nose. (02:09:15)
Continuity mistake: When Castor arrives at the airport, behind him there is a parked car in front of the building which on it reads "Welcome to Southern California International Airport", that disappears and reappears.
Visible crew/equipment: When Cage throws Pollux through the ceiling window, the support wire is seen in front of Cage as he's hanging from the edge.
Continuity mistake: On the speedboat at the end of the movie when Archer and Troy fly through the air, you can see foam on their clothes even though in the next scene their clothes are dry. (02:02:25)
Other mistake: When Troy (as Archer) goes to defuse the bomb, the #1 key lights up before he even presses it.
Continuity mistake: In the scene where Cage and Travolta are fighting on the dock, Cage stabs Travolta with the speargun (before he fires it). If you look at the spear after Travolta is stabbed, there is blood on it. Then in the next shot, the spear is suddenly clean.
Continuity mistake: When John Travolta is shot on the carousel at the beginning of the movie, the shot enters his back near his collarbone. When the camera moves back a second later, the bullethole is much lower.
Other mistake: At the prison, when Sean Archer (as Castor Troy) is talking to Pollux Troy to find out where the bomb is, Pollux hands him a cigarette. Never lighting the cigarette, in the next shot the cigarette is lit and he is smoking from it.
Factual error: The premise of the film is swapping the faces of the Hero and Villain. We can see the whole face of Sean Archer is intact in a water tank, which includes his eyelids and lips. When Castor Troy wakes up and confronts the doctor, despite his face being missing, he still retains eyelids and lips, which isn't possible as they would be missing. This should result in Castor having exposed eyes and teeth. (00:46:47 - 00:48:08)
Chosen answer: Although they were on the same side, Troy is currently posing as Archer, which means he would have to do everything that the FBI would expect Archer to be doing. The whole point of the raid was to take out Archer, as well as Troy's gang. He would have rather risked killing part of his own gang than risk exposing his identity to anyone else.
Casual Person
That doesn't really make sense. In the scene, he goes out of his way to shoot him and smiles while doing so, carefully and slowly. Was not a collateral damage situation. The question is why he deliberately goes out of his way to kill him.