Steps to reproduce:

1) Download attached project 'BugReport_Physics_Raycast.zip' and open in Unity
2) Open scene 'Scene' and press Play
3) Select 'Player' gameObject and change the position of X axis in the Inspector window
Note that physics.Raycast hits ghost collider

Expected result: Raycast should detect updated gameObject with Character Controller attached (check attached video 'expected.mp4')
Actual result: Raycast hits ghost collider (check attached video 'actual.mp4')

Reproduced with: 2017.1.0b2 2017.1.0f1, 2017.1.1p2, 2017.2.0f1, 2017.3.0b1

Note that Raycast does not hit a ghost collider if Character Controller on the gameObject is disabled and Capsule collider is attached

Physics.autoSimulation definition was included from Unity 2017.1.0b2