In a tank, the juice will cook around the coils, and sometimes, especially after a refill, you'll notice different shades to the color, or the tanked/cooked juice and the fresh juice. Just give it a shake to mix it together.
Ingredients do separate, and that is why it's recommended to shake your juice daily as well as right before filling your device. If it sets in the device overnight, it doesn't hurt to twirl or shake to mix it together again.