Steps to reproduce:

1. Open attached project
2. Open 'Firenze_santacroce_sunny' scene
3. Open 'Navigation' window to observe the navigation mesh carving edges (Menu/Windows/Navigation)
4. Focus the the player in the scene by double-clicking the 'Player' GO in the hierarchy
5. Notice the thicker edge between Player (green cube) and NavObstacle (red cylinder). (Pointed out the edges in the captured repros. See below)
6. Play the scene.
7. Click on the other side of the thicker edge, notice the player does not go through it, instead walks around that edge

Note: Disabling NavMeshObstacle solves the problem.

Couple of captured repros:
http://screencast.com/t/bacXT0lR819
http://screencast.com/t/R8MqiqWx