Iron_Cedar Ok, I dled the lot and took a look. From what I can tell, it looks like 3 tiles are blocked. And it looks like it's the handrailing above is causing the blocked tiles. There is nothing there that is visibly intruding into the tiles. Why? Idk, all I can say is that it's happening. And the handrailing is acting a little strangely. Every time I try to delete one round section (quarter circle) using shift hammer, the entire half circle handrailing on that end deletes rather than one half. I tried redrawing them individually and they kept doing it. That is not how that should work. It may be connected but idk for sure. All I can really say is that when you delete the handrailing above, the tiles become unblocked, and you can use the tiles.
So, for a more permanent fix, you might try reducing the open space in the above atria, so it doesn't extend over the rooms underneath or reduce the rooms by one tile width, so the walls below are not seen looking down. Since you've already found a workaround, you might just want to go with that as it will be a lot of work rearranging things due to the round sections.
Sorry I can't help more. Hope this helps.