I may have come across that before. I want to say its linked the the papyrus VM being heavily loaded when a settlement location loads. I can't remember if I have ever seen that behavior when walking into a settlement. I'm pretty sure its only when fast traveling. Remember when fast traveling, most often, the engine is loading 25 cells (default uGridsToLoad=5) at once. Usually unloading the settlement and returning fixes the issue.
I remember one time I saw a settler that was snapped into an animation marker moving about the settlement. I have seen settlers sleeping in mid-air nowhere near a building. This stuff all fixed itself eventually. It wouldn't surprise me if the engine's item placement system is put on hold when loaded and looking to free up some resources. Similar to how settler AI is the first to go. This is likely a vanilla system issue and would require some deep FO4 RE (reverse engineering) knowledge to be able to fix it.
There is also a similar issue where a building plan places an invisible object with collision. These do not go away with a location reload. They will go away if you find the plot placing the object and either deleting the plot or changing the building plan. If you come across any of these, notify the addon pack author so they can fix it.