When you add a new hue light or bulb to your hue system, you must edit your scene to include that new bulb. The bulbs that came with your hue system are automatically included in all of your scenes by default.
Think of your hue scenes are preset light configurations. When you edit them, you set the color and the level of brightness for each bulb and save the scene, then every time you press this scene it will sets all your lights to that configuration and will be used for various features through out your hue system.
To edit your scenes, press the pencil icon on the top right hand corner of your scenes page then select the scene you want to edit.
Then select Edit.
Select the up or down facing arrow to switch between light selection and color.
Make sure you have a check make in all the lights you want to be affected in this scene and adjust the brightness level. Once you have all the lights where you want them, press the check mark or Save button in the top right hand corner.
Now every time you select this scene, it will set your lights to the configuration you set them to.