POSSIBILE SPOILERS FOR NEWBIES...
I know the theories about The Faceless Man possibly being Soulblighter and all that jazz, but think for a second.
There were nine avataras in the Nine, but not every single one was mentioned in the game -- some go nameless.
Would it not be possible for these Avataras to be fighting with Bonecrusher or the Faceless Man in some irrelevant battles elsewhere on the map? I believe it is, considering that the main focus of Myth: TFL is on the Legion and its relative location, with rare mention of the other happenings in the world.
Maybe when the battle for Madrigal was occurring, an unmentioned Avatara of the Nine was fighting with, say, Bonecrusher in the Stair of Grief (notice how that location isn't a hot spot at all in TFL). Perhaps both of them were killed, or maybe just one of them, during the fight. The Nine DOES end up as the Three later in the game, remember.
Just an idea. :)