This Zendesk ticket (see bottom of comments) has a lot more detail. We never solved this one.

An AssetBundle manifest file gets wrong dependencies to other AssetBundles, which isn't actually referenced from the assets in the AssetBundle.

This issue occurs when a reference to an object stays in the m_Modification field of the prefab.

Steps to reproduce:

1. Change the Asset Serialization mode in the Editor Settings to "Force Text".
2. Create a script which has a GameObject[] list property.
https://gist.github.com/keijiro/3d2ca854d014a470d8de
3. Create a prefab named "Prefab1" that has the script above. Set the AssetBundle name to "prefab1".
4. Create an empty prefab named "Prefab2". Set the AssetBundle name to "prefab2".
5. Add a reference to Prefab2 into the prefabList property in Prefab1.
6. Change the size of the prefabList to zero.
7. Build AssetBundles.

Then see prefab1.manifest. It has a dependency to Prefab2, even though the reference to Prefab2 was removed in the step 6.