Summary of discussion: This behavior is the same as 4.x, but in 4.x it would miss small colliders which 5.0 got better at due to new elevator handling code in PhysX 3.3. This is by design, and won't be changed for 5.0 now.
However, it does seem like a desirable change to not collide with any child colliders. This could be implemented in ControllerContactFilter::preFiter. Consider this for future releases.

To reproduce this bug:

1. Open the attached project
2. Open 'CompanionCube' scene
3. It has a cube with rigidbody, character controller attached
4. Press play
5. Move() is called on character controller
6. The cube should move down slowly, but instead flies up

Works as expected on 4.5.x