Other mistake: On his own computer, Sean looks up his son's file, which states the boy died immediately and his date of death was September 9th, 1991. When Eve and Castor (as Sean Archer) are at the cemetery, the date of death on the headstone is September 24th, 1991. (00:21:15 - 01:14:50)
Other mistake: When Troy (as Archer) goes to defuse the bomb, the #1 key lights up before he even presses it.
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.
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)
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.