Steps to reproduce:

1. Create new project
2. Add cube object to scene but don't save the scene
3. Make prefab out of it
4. Open prefab editor
5. Disable auto save
6. Make any changes and save them using ctrl + S
7. Notice dialog asking to name the scene

Even though in top menu ctrl + S technically says "Save Scene" it's still little confusing as while in prefab mode you're not seeing scene. This also creates noise (especially when project is using VCS) while performing prefab save operation using shortcut

Reproduced with: Version 2018.3.0a2 (e9113db2e9bf)
Thu, 14 Jun 2018 21:56:37 GMT
Branch: prefabs/improved