Open the attached project:
1. Open the attached project.
2. Go to Bundles > Build.
3. Check the Console:

Assertion failed: Assertion failed on expression: 'srcFileInfo.temporaryObjectIdentifier.localIdentifierInFile == localIdentifierInFile'
UnityEditor.BuildPipeline:BuildAssetBundles(String, BuildAssetBundleOptions, BuildTarget)

Reproduced with:
5.5.0f1, 5.6.1p3, 2017.1.0b9, 2017.2.0a3

Notes:
- To avoid the issues go to Test > Run (Windows).
- Check the user patch (attached in this case) (1:50 AM).
- Full paths are always checked first to avoid a short name blocking a scene. For
example if you have in your build settings:

A/A.unity
A.unity

The latter couldn't be loaded. With this change, "A" will load the second, and only
"A/A" will load the first.
- Having two scenes with the same filename in one bundle would cause errors when
building the bundle.