I'm mostly into close combat (I don't snipe everything away that moves) so I'm pretty sure I only attack the hostile folks.
Well, that doesn't make much sense, if you reach a close distance of Follows-Chalk then he will initiate dialogue with you after he's sneak killed a White Leg.
This is your own fault though, not the developers, you went in too hot headed and just started murdering left and right without consideration.
And when you do kill Follows-Chalk you will get a text saying QUEST FAILED: [Quest name here], so that should have been a hint that something went wrong.
Follows Chalk is also dressed vastly differently than the White Legs.
Finally, use VATS as a scanner to see what is hostile and what isn't before you open fire.
So again, the fault is not on the developers part, it's on yours.
You didn't save often enough (which you should) and you killed without thought (which you shouldn't).