As a pianist comes to the organ, one of the greatest challenges he or she faces is independence--the ability of the hands and feet to operate independent of one another.
The most troublesome combination is the left hand and pedal. The brain tends to equate the motion of these two parts. When the pedal line moves to the left, the left hand tends to do the same. When the left hand lifts, the feet would do likewise.
Emphasizing the left hand and pedal combination in practice will help you develop a greater degree of independence.