Reproduction steps:
1. Open the attached project
2. Create an empty GameObject A
3. Add "UndoBugScript" to A
4. Create a GameObject B as a child of A
5. Add any component to A
6. Press CTRL+F5 to run code that makes B a root object without registering an undo operation.
7. Press CTRL+Z to undo the component addition from object A.

Expected behavior: B should remain a root object.
Actual behavior: a new B object is created as a child of object A, a second B object still remains in the hierarchy, selecting either of them highlights both

Reproducible on: 5.3.7p1, 5.4.4f1, 5.5.0p3, 5.6.0b3
Tested on windows 10;