This has been happening to me non-stop on a new mission. I've built an elaborate set in the sky (about 100 absolute y), using platforms and building blocks as the floor. Mostly, there are 500 x 500 or 100x 100 platforms, used as ceilings and floors.
When I put an npc contact on a map using any number of triggers, the npc doesn't spawn, or he spawns on the ground or up on top of the ceiling. I don't know where he is. I've used reach markers up close to see if he is falling through the platform, but no.
But, if I take that npc and sometimes move him 2 feet away from the intended spot, he will spawn just fine.
The obvious question: Am I using relative to geography or terrain on a non-flat map? Yes to non-flat map, but everything is set exactly as it should be with y relative to absolute zero. Either something with the spot on the platform or something about the underlying terrain is pushing my npc who knows where.
Anyone else experiencing this? I'm pulling out my hair just to get the npcs in the spot that I put them, and I'm afraid to move them one inch, in case that new spot is a problem for spawning.