Reproduction steps:
1. Open the attached project;
2. Open the scene "BugDemo";
3. Enable "Shows NavMesh" in the Scene window;
4. Enter Play mode;
5. Change the height of the object "Capsule Obstacle. My height affects hole.";
6. Observe the view;

Actual result: when the height of capsule is changing, the carve in the NavMesh is also changing.
Expected result: the NavMesh carve should not be related with the capsule height.

Note: the bug is happening when the NavMesh is with an particular "up direction" rotation (x axis = -90). If the NavMesh has rotation x axis = 90, then the carve is not related with the capsule height.

Reproduced with: 5.6.0b1, 5.6.0p2, 2017.1.0b1

Cannot be tested with 5.6 alpha and older versions because of NavMeshDataInstance class.

Verified with 5.6.1p2 and 2017.1.0b6 versions.