Reproduction steps:
1: Open scene "BlastLevelScene"
2: Press play
3: Wait till animation loop ends or Disable/Enable "MetaGameRoot".
4. Exit play mode.

Expected result: Everything will work fine, no problems will be detected.
Actual result: Assert appears: Assertion failed on expression: '(m_RendererData.m_IsVisibleInScene && IsInScene()) == m_RendererData.m_IsVisibleInScene'

Notes: This might not appear on first try. In that case, reopen project and/or change Culling Type and then set it back to "Based on Renderers".
It works fine without NavMesh, so you can remove it. The number of asserts might increase if prefab is selected when entering play mode.

Reproduced on: 5.5.0f3, 5.6.3p1, 2017.1.0p5, 2017.2.0b8, 2017.3.0a5.