Do you pound the pedals with much force or do you depress them with just enough energy as needed?
I know what most people think: "Of course I play very softly on the pedals".
But is it really the case?
Sometimes organists are not aware of the big movements they're making with their hands and feet. It comes so naturally to them.
If you want to be sure, place a mirror where you could see your feet, listen to the sounds your feet are making, and even record yourself.
This will tell you if your playing lacks precision because of the excess force you might be using for pedal playing.
Remember, Bach was known for his playing to have been effortless. Efficient movements of the feet were certainly part of this.
Look at the mirror. It helps.