We are facing the same issues with my friends. Basically, when loading the game, everything looks fine but then after some in-game time, some items are displayed above where they were built (on the floor below). However, I am still able to interact with the item if I stand where they are supposed to be.
For example, we have two chests on the second floor but I see them on the first floor and can still interact with them from the second floor (no interaction message is displayed so i just press the button).
I do have a theory and would like to ask you guys: how/where did you build your base?
We built ours on the oak fence but the posts don't have the same height so that leads to parts of our base being "in the air" (no anchor from below). I think that may be an issue.
ps: sorry for my english, not my native language.