Steps to reproduce:
1. Open attached project "New Unity Project (2).zip"
2. Make sure the cube scale is large enough (20,10,20 is fine)
3. intersect the cube with the plane
4. Make sure the cube is marked as "Not Walkable" in the Navigation > Object pane
5. Bake Navmesh
6. Observe the inside of the cube on the plane having a NavMesh

Expected: If the cube is not walkable, there should not be any surface inside of it that has a NavMesh
Actual: The plane that is inside the collider of the cube is marked as walkable terrain for a NavMesh agent

Reproduced on: 5.6.5f1, 2017.1.3f1, 2017.2.1p1, 2017.3.0p1. 2018.1.0b1