Undo operation doesn't move some scene's objects back which are in parent object.

Reproduction steps:
1. Open the attached file;
2. Open the scene 'Scene';
3. Select all objects which are under the object 'DO NOT SELECT';
4. Move objects;
5. Press Ctrl+z;

Actual result: Some of the objects don't move back in previous location.
Expected result: All selected objects should return in previous locations after pressed Ctrl+z.

Workaround: when you select the parent object and then move objects, every object returns to it's location. Also, when you throw out prefab objects of parent element, undo operation works correctly. One more thing, if you delete prefabs from parent element and locate new ones from Assets window, everything works properly. But if you save the project with new prefabs and reopen the project, a bug shows up again.

Reproduced on 5.4.0b19, 5.4.1f1, 5.5.0b5.
Tested for regression with Unity 5.2.3p3, 5.3.5f1.