I've just checked the stats screen in my Pip Boy, and under "Crimes" it says that I've committed 3 murders. After looking through my save games, I can say that it is because I killed some of the synths in final room of ArcJet Systems, the room where you get the Deep Range Transmitter. This surprises me because killing any of the synths before does not count as murder, and the synths in the final room are hostile by default. Is there any lore reason behind this phenomenon, or is this just a bug, or something else? Please don't give a detailed answer if this involves spoiling me for the rest of the story, my progress in the game is only to the quest where you rescue Nick Valentine, which I haven't completed yet. I also haven't joined the Brotherhood yet, the mission to retrieve the transmitter was actually the last quest I finished.