In Navisworks to optimize performance, all geometry is drawn using triangles. If you set the Render Mode to Hidden Line or Wireframe you will see how we draw your model.
Clash Detective will report the minimum distance one of the objects will need to move so the Clash no longer exists. With a Hard Clash this distance sees the intersecting triangles as separate objects, not as part of the whole face.
This is a screenshot of a line intersecting a 6 sided object with the render style set to hidden line. Notice that each side of the object is made up of two triangles. Taking a point to point measure from where the line hits the surface to the nearest edge of the object, it is 0.24m.
However, the distance reported in the clash result is 0.06m. Taking a point to point measurement from the point where the line hits the surface to the nearest edge of the triangle it intersects, it is 0.06m, which explains the distance value in the clash result.
You can get round this by using a type of Clash Test called Hard (Conservative), this is readily available in the 2013 release but for 2012 and earlier versions you need access this by going to the Application Button > Options > Interface > Developer and check "Show internal properties". When you go into Clash detective now you will have an additional test type named "Hard (Conservative)".
This reports all pairs of items, which might clash. This may give false positives in the results, but it is a more thorough and safer clash detection method.