Select a fixture in the layout in the cener of the view. The fixture will get a red border to indicate selection.
Only fixtures with programming on them in a scene will be controlled by the scene. Fixtures are not automatically added to a scene when the scene is created. Even if you want a fixture at 0%, you must select the fixture and add it at 0% for it to be included.
Once you add control of a parameter to a fixture it will get a blue border.
When creating a scene, selected fixtures are set to full intensity so you can see the programming, but this isn't stored in the scene unless you specifically set them in the Colour group.