Just been testing this out in debug mode as noticed it in my normal save. There is another warehouse in the same town that suffers from this. Its hit and miss on fixing it. The warehouse by the trailer park, I used the very small area as a temp base upstairs, then built out the floor completely and slept which appeared to fix it. Yet in debug mode its having no affect. Same with the above warehouse. Was going to make it the main base and the side be a pool room but now I want to move on due to the issue the warehouses appear to have.
I don't know if its relevant but in debug mode if you look at the area in ChunkDebugger mode you can see it defines the open space as outside, which I assume is why it screws up when you then try to lay flooring on it.