If a npc spawns on top of your bed while you're sleeping, would it be possible to find out where they came from or why they appeared? It's a custom bunker I built in GECK and linked to the wasteland and the 'intruder' was a Brotherhood of Steel Paladin. I began by checking the bed's properties to make sure it's player owned and doesn't have a script attached. (It's player owned and no script)

After scaring the crap out of me with his sudden appearance he said "Good to see you!" and left the bunker immediately. I followed him some distance outside until he ran into a group of enclave soldiers a couple of cells away from my bunker entrance, then they all died when a couple of cars went nuclear (stray missile or bullet probably.)

This sounds like Paladin Hoss.

My theory right now is that there is an odd glitch in the .exe now and then, and you tend to see it kick in when you wait/sleep or maybe fast travel or hit a load door. An NPC sorta switches onto a package that it shouldnt be on at that time, such as a follow package, in this case. And it warps to your location because of it thinking its supposed to be following you.

Since he's now dead, hopefully you won't have any more um, visitations!!!! haha.

You were right. I managed to reload a save game before the brother nuked himself and followed where he went. We both died in several places and I ended up using god mode to run ahead and clear the way. He ran to the river and followed it south along the West side until he got to Wilhelm's Wharf. Next to the wharf is a sewer tunnel which he entered, and that took us through Hubris Comics. We came out at Mason District where he then took the Metro tunnels to Falls Church. Once there he rejoined Paladin Hoss. I then loaded the save game again and fast traveled to Falls Church, Paladin Hoss was alone so that's definately where he came from.

It may not be that rare, and I've heard rumors of them stealing items out of your house (but I don't understand how that would happen if the NPC was not in combat, i've personally not seen them snag stuff unless attacked).