AssetBundleManifest.GetDirectDependencies Phantom Dependencies

Using Unity 5.5.2p4

I wondered if anyone had come across AssetBundleManifest.GetDirectDependencies() returning phantom dependencies? After building an asset bundle we generate our own manifest (project started off in Unity 4 before the ab overhaul) which includes the direct dependencies (generated by calling AssetBundleManifest.GetDirectDependencies()). However, it seems to include phantom results for which there is no logical reason/association for it to included.

We store all our assets in one prefabs scene from which we generate all our bundles. I've been through every asset in the phantom dependency bundle and manually selected all dependencies using the context menu in the project window. There are no references whatsoever to any asset in the alleged bundle (which only contains a handful of textures). It's almost like Unity is keeping cached junk somewhere that is invisible. I deleted the Library folder and reimported everything, but the problem persists.

With the large prefabs scene open, I also selected every (texture) asset in the project that would be included in the phantom bundle one by one and chose Find References In Scene. It came up empty for every texture.

Has this ever happened to anyone else?

For now I have a workaround to filter out the phantom results that are known to be false, which prevents those bundles from being loaded into memory. Just wondering if it's a bug in Unity.