So I'm puzzled and confused.
Running fallout 3 with vanilla settings the only changes made: the multicore fix + darnui fonts in the ini.

Mods: Darnui a11+hotfix

I cleaned all the dlcs with fo3edit +removed identical to master+undeleted references.

The odd bug I have is after about 1 minute in game I have a slaver guard spawn next to me.
He always have the same gear, police baton + leather armor.
He has no dialogue options, always neutral.

When I use mods that lets me start outside the vault I will after about 5-6 hours in game time,
have 2 npc's spawn in same cell as me, the ferry man for point lookout doesn't matter where I am, tenpenny tower, rivet city, megaton or some weird shackle in the middle of the wasteland.
Right after the ferry man the woman will force me into a dialogue about her lost daughter. (don't even have to speak with the ferry man for her to force me into a dialogue)

This issue exists even after reinstalls of the game, and what not. (applies to both win 8+7)
And yes I do have GOTY, and i don't have fose activated.