Well, I can't find the gotchas thread and I don't know if this has ever been covered before, but this is a minor gotcha. It won't crash the game, but it's damned annoying anyway.

Let's say you have two interiors. Interior A, and Interior B. In A you have an NPC or a door or anything else that can be targeted. In B you have a subspace to divide two levels split by a ladder through the floor or something. That subspace happens to encompass the door that leads from B into A. If you quest marker anything inside A the markers will malfunction and be pointing off into nowhere with a green marker. Even if you're out in the wilderness somewhere. Move the subspace so it no longer encompasses the door, and the markers begin working as intended - until the player steps into the bounds of the subspace. At that point the markers fail again.

I was racking ye olde brain trying to figure out why some markers in a quest weren't working right, then thought about the subspace and decided to confirm by moving it away from the door. BAM. Fixed it right up. Of course, that isn't really a solution if the subspace is necessary to make NPC navigation work right since the door will no longer be covered.

Good catch, but why would you need a subspace on a direct entry, leading to an interior, which you intend an NPC to pass through? Encasing just the door or the area around a door is never a good idea, and ideally you should try to contain as much of that level as possible within a single subspace (even if it requires a 10240x10240x512 block that's angled on three axis to fit around a sloping corner, and is partially sticking though ground that is not traversable). If an interior has no other doors, it probably doesn't need a subspace. I think the problem you are talking about stems from some of these.

Well the problem is that the interior has a section added in a vanilla cave. There is a hole in the floor with a ladder leading to the part down the hole. There is a small portion of area down that hole, and in this area is where the door to the next interior is. So that section is encased in a subspace so that NPCs in there will use the ladder to climb up/down the hole. The other two exits, provided by vanilla, lead to Tamriel and a basemant in Bruma. It's probably a somewhat unique situation and edging the subspace back off of my new door solved the problem well enough that everything is working properly except for the markers when the player finally enters the subspace. By then their destination is obvious though so it doesn't matter.

I suppose if something continues to end up being strange I could add an XMarker directly above the new door and outside the subspace and simply target that, taking advantage of the fact that the local map won't be able to tell it's over someone's head.