Sorry to say this is a common bug that has impacted many players who purchased the Special Edition. I've got it myself .
After a certain amount of hours played (40-50 for me) named NPCs start materializing in the twilight zone, rather than the main gameworld. Not sure if it's based on a saving issue, but to minimize it I would not fast travel or hard save, just leave your game in sleep mode when your session ends
Bethesda is aware of the issue and supposedly working on a patch. However the Beta testers are reporting it's still not fixed yet so.....might be a while before we've got a solution. Worst part is that saved games may not be fixed, so a re-start might have to happen.
Given the type of glaring issues SE has, I'm wondering if BGS just "assumed" the game would be fine.... Seems like the pre-release QA testing needs to expand outside of the shop more, this has got to be embarrassing especially since the game is not new to them...
If this happens on PC version is there any way to use the console or anything to move the NPCs?