Before the terrain editing update, basements would always, and forever, sit beneath the foundation. I wanted to add a basement to my Vacuous Green house - because money vault - and where the basement extended beyond the walls of the floor above, it was flattening the terrain to that height.

I could add a basement to the original pre-built house no problem.) It's because of the new terrain tools. (Play, this probably isn't your bug which seems like a bug. That's not a bug, and it's not related to any specific lot.