An AssetBundle with only one scene has a bigger size than expected

Symptoms

• An AssetBundle with only one scene has a bigger size than expected, but all the GameObjects in the scene are in other AssetBundles. 
• If I edit the manifest file, it looks fine.

Cause
The AssetBundle which includes only the scene also includes the default shaders. It is showed on the Editor.log as unity_builtin_extra.

Resolution

• Create a new Standard Surface Shader, add to another AssetBundle and rebuild the AssetBundles.

• Download the built-in shaders from http://unity3d.com/get-unity and include those shaders in your project. Change the first line of the built-in shaders from Shader "Skybox/Cubemap” to Shader “AssetBundles/Skybox/Cubemap”. Add them all to an AssetBundle and assign to your objects.

More Information
http://forum.unity3d.com/threads/custom-shaders-and-asset-bundles-on-ios.144014/

This article applies to Unity versions 5.0+