Visible crew/equipment: In the shoot 'em up scene at the hangar near the beginning of the film, right after Tito and Wanda take down Pollux, when Troy shoots an agent in the stomach and the agent flies back - you can see at least two cable wires pulling him backwards. You can first notice the 2 wires when the agent is running in slow motion right before he shoots him. (00:14:15)
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: While Sean tries to prevent the jet from taking off, in the exterior long shots of the aircraft there are windshield wipers over two of the cockpit's windows, but in the exterior closeups such as when Castor brings Winters into the cockpit the wipers are gone. (00:06:35 - 00:10:20)
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.