There are 2 World Space canvases with different z coordinates. Hovering over the closest canvas element hits UI elements that are behind that canvas element.
To reproduce:

1. Open the project, attached by tester (GraphicsRaycasterBug.zip)
2. Open "main" scene if not open
3. In Play mode, hover over the parts where small buttons overlap the big button
4. Observe the outcome

Expected: hovering over the button that is in the World space does not hit other World space buttons that are behind it
Actual: Graphics Raycaster hits the UI elements that are behind other UI elements

Reproduced in 5.4.5p1, 5.5.3p2, 5.6.0f3, 5.6.1f1, 2017.1.0b5

By design: this defect is known and won't be fix due to the amount of work to be done on our part, the risk associated is also very high. The workaround is to put everything in one canvas, not ideal, but better than nothing.