How to reproduce with new project:
1) Create a new project
2) There create new prefab, empty game object and 2 empty scripts (js or C#, does not matter)
3) Assign game object to prefab and attach any script to it.
4) Then right click on prefab and select 'Export Package' and you will notice that it has all projects scripts attached, this is undesired. It is expected that it would only show scripts that are attached in asset.