I have a mod house I made that has an NPC living in one of the rooms there. For some reason I cannot sleep in my own bed, even though it is owned by me. The interior cell is marked as owned by player. But whenever I try to wait after hours, or to use my bed (again after hours) there is a popup comment that I cannot sleep while being asked to leave. As I said, the cell is edited to belong to the player, not the player faction. I also tried checking the PUBLIC box, and made sure the CANNOT WAIT box was unchecked. I cannot understand what I am missing.

Be sure to double check the ownerships:

Reference/Ownership/Faction/Player Faction Don't tick off any of the boxes.

CellView/Cell/Interior Data/Owner Faction/PlayerFaction

By chance have you created a faction for house mod that includes you and the occupants of your house?

Are you using any default AI packages that you have modified that results in others coming into your house that shouldn't be there?

I can't remember if Lock Lists affect this. If the NPC has the ability to lock a door, it may affect the trespassing rules. If that's what's doing it, then time of day would change things.

In the cell's edit screen, gotten to by right-clicking on the cell view window, I go to the Interior Data tab. On it I have owner listed as Player. The owner faction tab has been left blank. I have the box ticked that says Public Area below it as well. I did not create a faction for the NPC's and player, but did create a Merchant (house name) Merchant faction, which is necessary to make the merchant act as a merchant, and to own the chest they vend from. I did not issue a key for the house. My understanding is that doing so would cause the player character to have to pick the door lock every night to get in. I also made sure that the Can't Wait tab was left unchecked. Beats me what is wrong.

Follow the instructions I gave above removing the edits you made that conflict and see if that works.