Steps to reproduce:
1. Open attached project "TransformNavMeshPhysicsBug.zip"
2. Make sure to not have anything selected in the hierarchy
3. Enter play mode and observe the agent hit the door and not progress further
4. Optionally, Enter play mode when having selected something in the hierarchy
5. Agent will pass through both sliding doors without a hitch

Expected: Regardless of hierarchy selection, the agent will return appropriate position information and won't get stuck
Actual: If you have nothing selected in the hierarchy the agent will get stuck, the console will output the abnormal position of the agent

Reproduced on: 2018.1.0b6, 2017.3.1p1, 2017.2.1p3, 2017.1.3p1, 5.6.5p1

Notes: Does not reproduce if you set Collision Detection to continuous.
With discrete CD reproduces on build too.

Won't Fix: The Rigidbody in question is not Kinematic, which results in this glitch