Continuity mistake: When Troy (as Archer) arrives home for the first time, he's walking around his wife. When he says her name, his right hand is held up. From a different angle as he moves to her right, his hands are by his side. (00:52:50)
Continuity mistake: When John Travolta's daughter slams her bedroom door in his face, from one shot it nearly closes, but in another shot he blocks it when it's still got a long way to go. (00:54:35)
Continuity mistake: When Troy (as Travolta) is about to defuse the bomb, watch the timer, it goes down too slowly for the time elapsed. It shows 1:14 and 28 seconds later it only shows 1:04, not 0:46 as it should. (00:58:45)
Continuity mistake: After being told that Pollux was released from prison, Sean Archer (as Castor Troy) shouts that he's Sean Archer, then grabs hold of the bars above him, with three bars between his hands. Next shot, as the guard's foot is on his hand, there are only two bars between his hands before he lets go. (00:58:50)
Visible crew/equipment: When Buzz and Wanda stand in the outer room, in the first shot, the camera pans around and faces the agents' TV, showing the video feed of Pollux in the interrogation room singing about his tiramisu. On the agents' TV screen, the reflection of the crew's rather large black square screen is visible (on a stand) in front of the windows (to block window light and view of the crew/equipment) and just as the camera faces the TV head-on, a crouching crew member begins to stand (seen at the left side of their TV screen). (00:59:05)
Continuity mistake: When Castor Troy (as Sean Archer) turns off the video-cam and walks into the interrogation room with Pollux, the Coke has two straws, but next close-up there is only one straw as he turns off the microphone. (01:00:00)
Other mistake: In the scene where Archer (as Troy) escapes with Ivan Dubov we see their tracking blips still moving on the tracking monitor after their tracking boots have been removed. (01:06:35)
Other mistake: When Archer (as Troy) and Dubov are fighting with the guards prior to Archer escaping, we see two guards looking at a computer screen which has several prisoners names registered on it, including Pollux Troy's name. Pollux has already been released from the prison by this stage, so his name should have been removed from the prison's computer system. (01:06:50)
Continuity mistake: At Erehwon prison, during the cigarette incident, Sean (as Castor Troy) is knocked down, and while on the floor the side bar of his left magnetic boot breaks and the entire boot begins to fall off, but it's intact when he crawls to get the cigarette. (01:07:20)
Continuity mistake: During the prison breakout, when Dubov falls over the railing after being shot, in the first overhead shot he falls backwards, but next shot he falls forward (chest down). (01:11:40)
Visible crew/equipment: During the prison escape when Sean Archer (as Castor Troy) is running up the stairs towards an exit, a crew member's foot and lower pant leg can be seen in the upper right hand side. (01:12:25)
Continuity mistake: On the chopper, when Sean Archer points his gun out the window, in the shot facing him the window to his right is a double slide type. In the next shot, from inside the chopper, his arm is through a single window that flips down. (01:23:00)
Continuity mistake: When Jaime is screaming, Castor Troy (as Sean Archer) walks out to the front yard and the back tires/end of Karl's car is on the sidewalk, but when Karl is dragged out, the car is farther up the driveway. (01:24:50)
Continuity mistake: At Dietrich's, when the firing begins, Sasha grabs a woman and they both start running up the stairs, but a few shots later when Sasha yells, "Cas, be careful with him," she and the woman are still downstairs. (01:33:40)
Visible crew/equipment: During the raid at Dietrich's, when Sean (as Castor Troy) hangs on to the chain then grabs hold of Pollux, in the close-up Pollux's safety wire is visible in front of him. (This is not Sean's safety wire, as seen in the following shots.) (01:39:05)
Continuity mistake: At the church, just as the shooting is done with, Eve is leaning down with her hands covering her head. Then, in the close-up she uncovers her head and sits upright to look around, but in the next shot, she's still leaning down covering her head. (01:54:30)
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)
Continuity mistake: During the speedboat chase, when Castor Troy (as Sean Archer) shoots up the white speedboat that Sean (as Castor Troy) drives, there are numerous bullet holes on its starboard side. Four shots later, when he hits the box on the rear seat, those bullet holes on the starboard side are gone. (02:04:15)
Visible crew/equipment: When Sean (as Castor Troy) is doing the 'water skiing' thing, trying to hang on to the speedboat's chain, in the close-up the harness he wears is visible under his wet white shirt. (02:06:50)
Continuity mistake: On the speedboat, when the anchor comes loose from the boat's bow it takes with it a large chunk of metal and leaves a gaping hole, but next shot, as the anchor falls to the water, the huge hole is gone leaving only the bullet holes on the surface. (02:07:20)
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.