Steps to reproduce:

1. Open attached project "961051.zip"
2. Select "Assets/asset cube/asset.prefab" in the Project View
3. In the Inspector change the prefabs AssetBundle name to "asset" and extension to "bundle"
4. Press "ASSET BUNDLES/build all" to build the cube prefab asset bundle
5. Move "asset.bundle" to "Assets/asset cube" folder
6. Select "Assets/asset cube/asset.prefab" in the Project View
7. In the Inspector change the prefabs AssetBundle name and extension to none
8. Repeat steps 2 - 5 for "Assets/asset sphere/asset.prefab" accordingly
9. Enter play mode
both cube and sphere asset bundles will be loaded

Actual result: second asset bundle doesn't get loaded and error is thrown:
The AssetBundle 'asset.bundle' can't be loaded because another AssetBundle with the same files is already loaded.
Expected result: second asset bundle should be loaded, because it's a different bundle with different files

Reproducible with: 2017.1.2p2, 2017.2.0p1, 2017.3.0b8, 2018.1.0a3

Notes:
Providing CRC doesn't fix this
Renaming already built bundles doesn't fix this