Steps:
1. Create a new project
2. Add any script to Assets (default "New MonoBehaviour" is enough)
3. Add "GameObject -> Effects -> Particle System" GameObject to Hierarchy
4. Drag it to Project browser to make a prefab asset
5. Select Particle System instance
6. Drag and drop script to Inspector
==>
Restructure prefab instance dialog appears (expected: script is added as override)
7. Open prefab and drag script to inspector
Restructure prefab instance dialog appears (expected: script is added to asset and merged to instance)

Workarounds:
1. Drag script on top of prefab instance
2. Add script through "Add Component" button
3. Add other component and then add a script though Inspector

Take a look into attache movie for details