It’s perfectly normal for a few centimeters of water to remain in the upper chamber. This is because the Black Berkey filter elements sit on a rim, and water naturally cannot pass over this rim. In addition, the water pressure is very low when there’s only a small amount of water left in the upper chamber, which prevents the water from flowing through. This applies when the water level is still just slightly above the rim of the filter element.
You can discard any remaining water if you're refilling the top chamber of your Berkey water filter.