Repro steps:

1. Open "SpriteStencilBug" projects "Main" scene
2. Look at "UnlitStencilSprite" and "UnlitStencilMesh" in the Hierarchy window (One has a Mesh renderer and the other has a Sprite renderer)
3. Open the "UnlitStencil" Shader file
4. Change code at line 18 from "Comp Always" to "Comp Never"
5. Go back to the Editor

Expected result: Both of the cubes disappear
Actual result: One of the cubes disappear (The one with the Mesh renderer)

Reproduced with: 2017.1.0a6, 2017.1.0b8, 2017.2.0a1
Regression introduced in: 2017.1.0a6 (00315a6f23c0)
Did not reproduce on: 5.6.1p2, 2017.1.0a2, 2017.1.0a4, 2017.1.0a5