Can confirm, this is VERY annoying, particularly because so few people build that googling that this is the actual problem is extremely difficult, hard info to locate. In my case a double staircase leading from east to west, the 3 tiles directly over the southern most staircase are not considered inside. On the floor the stairs lead to (second floor in my case), building 3 walls to separate the area above the stairs fixes the issue, but it is ugly from upstairs. I spent hours breaking things.