Commander Burke isn't killed in the end.Never Found the Body, right? It is assumed that he saved Carnby and Aline by the moment they get attacked.
The reason the guns suddenly become lethal to the monsters, after the bullets just bounced off of them...Is also connected to the reason they suddenly fire tracer rounds. Essentially, since their going up against monsters of darkness, it logically means that the tracers act as Holy Hand Grenades - or at least, the closest thing Bureau 713 can get. The reason it's never explained is because, Uwe Boll being Uwe Boll, He Just Didn't Care.
The original writer of the script eventually worked on Alan WakeBlair Erickson, who was trying to write the original screenplay for Alone in the Dark before Uwe Boll went full retard mentioned that the perspective of the story would be told from "the eyes of a writer following Edward Carnby and his co-worker for a novel". The same year Uwe Boll's latest cinematic trainwreck is unleashed, Alan Wake was announced, with the main protagonist being... a novel writer. Coincidence?!