Steps to reproduce this issue:

1. Open the attached project
2. It has 'test' prefab
3. Prefab has 2 scripts: 1) MainScript 2) SubScript
4. MainScript uses: 1) this.GetComponents(list1); and 2) gameObject.GetComponents(list2) to get and add 'SubScript' components to lists
5. On Prefab toggle the checkbox "toggle me to validate"
6. Watch the log as it counts number of list elements:
this.GetComponents(list) 1 / gameObject.GetComponents(list) 0
7. Drag 'test' prefab into the scene
8. Toggle the same checkbox
9. Now log indicates:
this.GetComponents(list) 1 / gameObject.GetComponents(list) 1

Works fine in 4.6