1) What happened
m_InstanceID == 0 when adding assets

Not reproduced on 4.2.0f4 and 4.2.1f2 and 4.2.1f3
Reproduced on 4.2.1f4 and 4.3.0b1

2) How can we reproduce it using the example you attached
1 Open Unity and create new project
2 Import Character Controller package (in menu Assets->Import Package->Character Controller)
3 Close Unity
4 Open Unity and create new project - through menu File->New project
5 Import Character Controller package (in menu Assets->Import Package->Character Controller) - after importing notice error in console:
m_InstanceID == 0
UnityEditor.AssetPreviewUpdater:CreatePreviewForAsset(Object, Object[], String)