Tested this in build 120 but I assume it applies to previous builds as well.
- Create a new project
- Add a new object and set its layer (I have added NewObject2 - Lighting Layer)
- Select the newly created object in the scene view (optional, not selecting it doesn’t make any difference)
- Now delete the layer that the object is in (choose ‘Remove objects’ as well).
The object disappears in the scene view but the box that allows you to scale the object does not go away (you cannot scale or rotate the now-deleted object of course but its there), the ‘instance view’ window still shows the deleted instance.