Steps to reproduce:

1. Open attached project
2. Open scene "Scene"
3. In scene view, select three cubes by doing ctrl+click
4. Release ctrl and select plane to unselect previously selected cubes
5. Press Undo (ctrl+z)
6. Notice that not all previously selected cubes are re-selected

Not reproducible: 5.2.4f1
Reproduced with: 5.3.2p4, 5.4.0b4
Couldn't test on latest 5.4 beta due to http://issuetracker.unity3d.com/issues/scene-cant-shift-click-to-multi-select-objects-in-scene-view