Any assets located in Packages but referred to by asset bundles in the main Assets folder do not seem to get included in the asset bundle like other dependencies usually do. For example, if a prefab in the Assets folder references a shader in the Packages folder. The prefab is included in the bundle but the shader is not. This is despite the fact that selecting the prefab and choosing "Select Dependencies" will correctly highlight the shader in the Packages folder. This problem was found while working with the Post Processing package in a game that makes heavy use of asset bundles. See full bug report here: https://github.com/Unity-Technologies/PostProcessing/issues/766 In that particular instance there is a workaround with the Graphics settings, but in general I think this reduces the usefulness of packages anything other than Scripts.