Steps to reproduce:

1) Download attached project "BakedLight_And_Layers.zip" and open in Unity.
2) Open scene "TestScene".
3) In Hierarchy tab, check "Sphere_AffectedByBlueLight" and "Sphere_AffectedByRedLight" have different layers.
4) In Hierarchy tab, check "RedLight" and "BlueLight" Culling Masks.
Note: RedLight should lighting "Sphere_AffectedByRedLight" and BlueLight should lighting "Sphere_AffectedByBlueLight".
5) Bake lights.
Note: Both spheres being affected by both lights(see attached image "Lights.png".

Expected results : One sphere should be affected by BlueLight, other sphere by RedLight.

Actual results: Both spheres being affected by both lights.

Reproduced with: 5.2.4f1, 5.3.5p7, 5.4.0b24, 5.5.0a2