To reproduce:
1. Open attached Unity project "Template Layer Bug.zip"
2. Open scene "31th"
3. Click on a Prefab "Prefab" in Project window

Expected result: Only a white circle should be seen in prefab's preview.
Actual result: Every object in the scene that is assigned to the 31st layer is seen in the prefab's preview.

Reproduced on 5.6.0f3, 5.6.0p3, 5.5.3p1, 2017.1.0b1

Note: Open a scene "no 31th" and click on the prefab to see what its' preview is supposed to look like.
Note: every object assigned to the 31st layer will be visible in all of the prefabs' previews.

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Fixed in 2017.1.0b3