Yes, it is normal and not unusual for the last 1/2″ to 4″ of water to remain in the upper chamber. By design, the water must pass through very fine micropores within the elements in order to pass from the upper chamber to the lower. The lower the water level in the upper chamber, the lower the pressure available to force the water through the micropores. You might have noticed that the system purifies much faster when full than when half full. That is because there is more pressure.
During each cycle, the water left from the previous cycle mixes with the water from the current cycle and is then purified. You should not be concerned about the excess water during normal use however if you discontinue using your filter for a period of time such as during a vacation, it would not hurt to empty the upper chamber before departing.