The Scene contains a capsule collider and a non-convex mesh collider that are slightly overlapping. Physics.ComputePenetration should report that the penetration depth is quite small but instead it is reporting a very large value. If you slightly change the rotation/position/size of the colliders then the issue no longer occurs.

To repro:
1) Open attached project
2) Open Test Scene and enter play mode
3) Press S Key and see that depth is printed in console and on screen as 743.8444

Reproduced both in Editor and Standalone testing on OS X. Unity 2017.1.1p2.