To reproduce:
1. Open attached project "New Unity Project.zip"
2. Open "buttons.unity" scene
3. Enter play mode
4. Click on the button in game window Display 1 observe as the buttons presses
5. Click on the same spot where button is on game window Display 1, in game window Display 2

Expected result: button on game window Display 1 is not pressed
Actual result: button on game window Display 1 is pressed

Reproduced on: 5.6.1f1 5.6.1p2 2017.1.0b8

Not reproduced on: 5.5.0f3 5.5.4f1

Regression introduced on: 5.6.0a1 (you still can not press the button on the game window Display 2)

Notes: on 5.5.x you can not click the button on game window Display 2. Using canvas render mode Screen Space - Camera, getting same results.