The Scene activation switch is a special kind of virtual device. It's on/off state, as you've discovered, reflects the activation state of the Scene. If all devices are at Scene settings, then it is on. If any device in the Scene is not in its Scene setting, then the activation switch is off.
This activation switch is unusual because it can be used for On when it is already on, and used for Off when it shows being off. I don't know if this works correctly in a Dashboard. So for the case you are describing, you should be able to turn off the Scene lights by turning off that Scene switch, even if it is off already.
How are you controlling the Scene switch?