Steps to reproduce:
1. Create new project
2. Create empty GameObject in hierarchy
3. Add "Rect Transform" component to it
4. Create empty canvas object as a child object for the newly created GameObject
5. Make GameObject a prefab
6. Delete canvas within hierarchy
7. Remove Transform component from GameObject
8. Apply prefab changes within inspector
9. Press Ctrl-Z to revert these changes

Actual result: Crash
Expected: Deleted things get recreated

Tested and reproduced on:
Windows 10
Unity 5.4.0p2, 5.5.0a6

Not reproducible on:
Unity 5.3.6p3