Steps to reproduce:
1. Open attached project "SpriteRaycastIssue.zip"
2. Open Test Scene
3. Enter Play mode
4. Try clicking the button (the only sprite on screen)
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5. Select "testatlas" in the Project panel
6. Remove "spritesheet" from the Objects for Packing list, click to repack
7. Enter Play mode again - the button will work now

Actual result: no clicks are registered
Expected result: the button is clicked normally

Reproduced with: 2017.1.1f1, 2017.2.0f3, 2017.3.0f1, 2018.1.0a7

Note: with 2018.1 and 2017.3 it behaves differently - the sprite's alpha channel is ignored and the click works, but that still isn't the intended behavior