To reproduce:
1. Open attached project
2. Open scene repro - it has a character controller and a sphere on a plane. The character controller's Step Offset is set to 0.55, which is lower than the height of the sphere
3. Enter play mode and walk into the sphere
4. A console message prints out the hit.moveDirection values. These are wrong, as they output {0,-1,0} (meaning that the sphere is below the controller) while the player is clearly in front of the sphere

If you set the Step Offset to 0, the correct values are printed.

This is by design, as this is how the Character Controller works. If you just want the direction the controller is moving in, just use the vector you passed to the move function.