title says it all

How the NPC factions, or lack there of relates to the player helps a lot.
I ran into it while modding Fallout 3.
Doing the group faction right, even made the turrets in my dungeon friently, but capable of being set hostile in an instant using the right script commands.

I removed my NPC's faction data completly and it doesn't fix the problem

Note: some of the NPC's that teleport are Feral Ghouls

Have you created and checked the navmesh for your dungeon? It may be that the NPC's are placed where there is no navmesh, and then they "pop" to the nearest location which has valid navmesh.

My solution was to craft a faction or use a faction in each npc, if appropriate, which is friendly to the player.