1. Lack of direction. A lot of times people who just start improvising on the organ, have lots of wishes, and a lack of proper direction. They want to become very good improvisers in many styles. In reality it doesn't work this way. The more you can improve your focus, and simply work on a certain style or genre for a while, the better chances you have to succeed.
When you feel fluent in one style or genre, you can easily begin to explore additional styles or genres. So it is important to stay focused at only one goal at a time. Taking your daily baby steps towards this goal will increase your chances for success.
2. Being lost in this process. Many people don't know where to start when it comes to organ improvisation. There are so many method books and treatises and every one of them requires at least some knowledge in music theory. So it is very difficult to improvise well if you don't know basic concepts of music theory, harmony, and basic elements which constitute a musical piece.
If you want to learn to improvise on the organ, it is inevitable that at some point or another you will understand the necessity to learn music theory, harmony, and musical analysis. It is better to start this study sooner than later.
3. Inability to achieve the results. It may happen that no matter how hard you are trying to improve, no matter how focused you are, you are still not getting your results. Or perhaps the results are so small that when you start to think about your long-term goal, you may be thinking that it will take many years to achieve it. This might be very frustrating.
It may mean, that you are practicing incorrectly. You see, improvising on the organ is no different that learning to play a written down composition. The only difference is that you have to think and compose while you play.
But you should still apply the same practice principles as if you would be playing a real organ piece - slow tempo, practice in fragments, voice combinations, aiming on improving your technique and doing repeatedly over and over again.
Think about these tips and apply them in your improvisation practice. You may be surprised how fast your improvement will be if you remember your goal, deepen your knowledge of music theory, and constantly take incremental baby steps.
If you need help in practicing organ improvisation, check out my free improvisation mini course.