How to reproduce:
1. Download attached project file and open "Test" Scene
2. Open Window -> Physics Debugger
3. Select "Collision Geometry" in Scene Window Right corner
4. In Physics Debug Window, Hide Layers section select "Default" value (notice that one GameObject disappears)
5. Then select "Phsy1" (Notice that GameObject still appears)
6. Then Select "Everything" (Notice that GameObject still here)

Expected result: "Hide Layers" function should work with individual layers
Actual result: The scene included has 2 bodies one on the default layer, and one on a custom layer. The debugger hide layers feature works on the default layer but not on the custom layer

Reproduced with:5.6.0a2, 5.6.3p2, 2017.1.0p5, 2017.1.1f1, 2017.2.0b10, 2017.3.0a7
Not reproduced with: 5.6.0a1

Regression since: 5.6.0a1