I agree with the flare thing and actually enjoyed Brant trying to make sense of it(for the viewer?).The flare thing I thought made some kind of strange sense. Those soldiers are probably operating mostly on instinct, and if they see something moving, they're gonna shoot at it.
But there were a LOT of other contrivances in this movie-- the idea of these expert assassins going to a meeting with no idea what someone looks like, the fact no one else walked in while Hunt and Benji were doing their hallway trick, the fact Benji can so easily sneak into these underground control rooms or next to sensitive areas...
We could make off screen excuses I suppose for the other stuff. High profile people like this work on reputation and paranoia so as Kaiser Sose says, "the devil only sticks his head out once"(or rarely). Email, texts, other drops work better because the fewer people you meet the fewer that could betray you? The Hallway trick? Benji already had control of the building. Perhaps he locked stairwell doors and elevators so no one could come to those floors AND locked any room doors to prevent access into the hallway. As for Benji getting into sensitive areas we just assume he's as good at his area of expertise as Hunt is at his.
Or we just suspend disbelief, whichever is easier.