It doesn't! I was able to actually resolve the issue while talking to someone on the Discord. There were multiple patches across the lot, and it seems like what did the trick was making the whole lot into a room and deleting the flooring all at once (technically 2 because the pool area seemed to count as another room I had to save.)
I should mention that the lot is not originally mine but I removed their terrain and rebuilt the area because I liked the landscaping. The patches appeared underneath the original builder's houses and the pool when I deleted them. Building on top of some of the patches seems to add concrete tiles on the second floor and its borders like in the pictures in the original post.
I am not sure how to link stuff here from the gallery but the original lot is from Amn_Haze44 called Sulani Cottage for the Journey's End lot in Sulani. I uploaded a lot called 'Patches' (it is the same username as here) where I recreated how the lot looked when I deleted the houses and bulldozed the terrain (though for some reason there's two hills now). The other one is my recent progress in the same lot (I covered the patches with grass tiles which made me realize it might have been connected to this one).
I still want to know what was causing this though!