There are a couple of reasons why you find these problems:
1) Many people are right-handed and naturally they use their right hand more frequently than the left which in turn just makes the left hand under-developed.
2) A lot of people start playing the organ after having some experience with the piano. On the piano, the left hand takes the bottom stave while on the organ you have to train your left hand (and the brain) to play the middle stave.
So how do you strengthen your left hand technique? There are a couple of useful things to remember here:
1) You can practice special left hand exercises, scales, and arpeggios regularly. Over time this will help to make your left hand technique more developed. The goal here is to reach the same level of dexterity and independence with the left hand as with your right.
2) As you practice your organ compositions, remember to play the left hand part (and left hand and pedals combination) many more times than with the right hand. For example, if you normally play an episode with right hand 10 times, than play it 20 times with the left hand. The same is for left and pedals combination.
3) I have noticed that some organists play hymns this way: soprano and alto is played by the right hand, tenor and bass is played by the left hand. At the same time, the pedals double the bass.
I hope you are not playing this way because it greatly slows down the development of left hand and pedal independence - left hand has to learn to play different melodic lines than the feet.
Do you want to make your left hand as strong as the right hand? Then start applying these tips in your practice today. It will not be long before you start seeing some tremendous changes in your technique.
By the way, do you want to learn my special powerful techniques which help me to master any piece of organ music up to 10 times faster? If so, download my video Organ Practice Guide.