I created a house and it has been working fine but I noticed that I now have a ghost named sankir (something like that) in my basemant. He does not show up when Im working in the creation kit. I went to the house in game and now sigrid is in there too, working away on the enchanting table. I cannot find either of them listed as an object added to the house. Anyone have any ideas as to why these npcs are spawning inside the house?

My guess is that you copied the interior from another cell (perfectly normal), but there are some things that are telling the NPC ai that it's ok to enter because it thinks it's still part of the cell you copied - for example, if you copied Breezehome and didn't change the Location, if your spouse was settled in Breezehome, she might show up in your new cell. Right click the name of the cell on the cell list and go to edit. Check the Location on the Common Data tab, and make sure it's not registering as someplace it shouldn't be (there's usually a default Hold location for whatever Hold you're in - usually a good thing to replace it with). Also check the Interior Data and Encounter Zone (although I think Encounter Zone is more for the Radiant Quest generator.)

This happened to me! This happens when you accidentally change one of the default AI packages to be specific to a certain cell. Just copy the package and rename it something specific to your mod, like "MyAIPackage" so that every NPC that uses that default AI package doesn't hang out there.

Find out which AI package you changed by going to Character>Packages and seeing which one has an asterisk.

Yes, you'll need to remove any x markers and other markers that tell NPC's you don't want there.

oooh i was messing around with the ai packages when this started happening. Thanks!