Revealing mistake: When Loomis comes upon Castor grieving over Pollux's body and says "Sir, why are you so upset? Its just Pollux Troy", you can see discoloration of a lump on his forehead which is makeup covering the blood pack where Castor will shoot him.
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)
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: After leaving the Hummer, when Sean gets into the chopper the cabin interior changes in the following shots. This includes the windshield, hand grip, wall, etc.
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)
Continuity mistake: At the airport hangar, after Castor reloads, in the close-up Sean is kneeling beside a crate with a large black/white SCI air freight sticker. In the overhead shot, when Castor Troy aims the gun at Sean, the sticker is gone. Debris also disappears. (00:15:35)
Visible crew/equipment: When the red boat has hit the barrier and Castor Troy and Archer fly through the air, you can see a wire attached to the front of the boat just for a split second, then when it falls in the water and explodes.
Continuity mistake: After Sean looks up his son's file on the computer, and types "case closed" on Castor's file, he rubs his head with his right hand in the close-up, but next shot he is rubbing his head with his left hand. (00:21:20)
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)
Continuity mistake: After the jet crashes into the hangar, Sean Archer runs up the back end of a police cruiser, whose three blue flashing lights are completely shattered. In the next shot facing him, when he reaches the car's roof, two of the blue lights have repaired themselves. (00:13:45)
Continuity mistake: When Castor (as Sean) grips the speargun, in the following close-ups, the sling ends (with its wishbones) differ - just note the rings around the rubber ends.
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: 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)
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.
Continuity mistake: After Sean types "case closed" on Castor's file, Dr. Miller walks into Sean's office and holds out Pollux's Zip Disk for Sean to take. In the next close-up, the Zip Disk has flipped over and faces the opposite way.
Visible crew/equipment: When Archer gets into the chopper and takes off, next shot is of the chopper flying towards the camera and it is not Archer who is flying it - the chopper pilot wears head gear and a mic. (00:11:40)
Continuity mistake: After the incident with Karl, when Castor (as Sean Archer) and Jamie are in the living room, he opens the cigarette case and offers her one. The way he holds the case noticeably differs between shots.
Revealing mistake: At Erehwon, Sean (as Castor Troy) is given steel magnetic boots to wear, for the prison's important security feature. There is a close-up of these heavy duty boots during his 'exercise'. Then, when he is taken to the clinic there is another close-up, and there are a number of changes to the boots style. More importantly, one of the side "bolts" has fallen off, revealing that it was merely glued on the prop boots.
Revealing mistake: Just as the red speedboat heads toward shore, before it crashes, the white and red truck cranes are on the dock and the white crane arm is angled backwards over the dock. In the shot facing the speedboat, as it explodes, that crane arm is now angled the opposite way, over the water, since it was used in the stunt.
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)
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.