Steps to reproduce:
1.Create a new or open an existing Unity project
2.Create an Empty Object in the Hierarchy
3.Enter and exit Play mode
4.Undo until the created game object disappears

Expected results:
Created object disappears after one undo action
Actual results:
Object disappears after three undo actions (exit Play mode -> enter Play mode -> Create Empty)

Reproduced in: 2017.3.0b3, 2017.2.0f2, 2017.1.1p4, 5.6.3p4, 5.5.5f1, 5.5.0f1