To reproduce:

1. Open the project, attached by user (ColliderDistance2D_Bug.zip)
2. Open the "Scene" scene if not open
3. Move the capsule around inside pentagon
4. Observe the distance shown by white line

Expected: points and distance between the points are calculate correctly by Physics2D.Distance
Actual: Physics2D.Distance returns incorrect distance between the CapsuleCollider2D and PolygonCollider2D, when the capsule's origin point is inside the polygon

Reproduced in 5.6.0f3, 5.6.1p1, 2017.1.0b6, 2017.2.0a1

Could not test for regression, because Physics2D.Distance was introduced only in 5.6

By design: When calling the Distance function, it gives you a solution for a single step only. In a lot of cases, that will solve an overlap but as the cases get more complex, multiple iterations are needed.