Steps to reproduce:
1.Open attached project
2.Press play
3.Observe as you can not select the child buttons (you can if you move your mouse to the left bottom corner of the screen)
4.Exit play mode
5.Disable "Main" game object from the hierarchy
6.Press play

Expected result: buttons click positions are on the buttons
Actual result: buttons click positions are in the left bottom corner of the screen

Reproduced on: 5.6.0f3 2017.1.0b1

Not reproduced on: 5.5.2f1

Regression introduced on: 5.6.0f1

Notes: if you create game object and set parent with a script ("Main.cs" in the project) the issue is here, but creating game object manually solves the issue.

Screen recording attached.