Steps:
1. Create new GameObject.
2. Make it a Prefab.
3. Open Animation view and click Create Animation.
4. Click the red record button in Animation view.
5. Set GameObject's scale to 2,2,2 (fields should become red to indicate it's temporary animation values)
6. Click the Preview button in the Animation view to exit Animation mode.
7. Note that GameObject's scale is 1,1,1 (correct) but it's an override (bug)
8. Click the red record button to go back into animation record mode.
9. Note that the scale is 2,2,2 again (correct)
10. Right click on scale property and select "Apply to Prefab 'GameObject'".
11. Select the Prefab Asset and note that the scale has changed to 2,2,2 (bug)