1. Delayed sound. I have played a few organs which have a curious feature - when you depress the pedals, the sound appears a moment later, even later than those on the manuals. This is due to the fact that either the pedal action is different or the tallest pipes need more time to speak.
Solution: Depress the pedals and release them a moment earlier than the manual parts.
2. Distances in different style pedalboards. It's easy to miss the notes on the pedals when you are used to one style of pedalboard (radial, flat etc.) and you suddenly have to play an instrument with a different pedalboard.
Solution: Play as many different instruments as possible. This experience will help you adjust to the new pedalboard much faster.
3. Bench in historical organs too high. In this situation, you can barely touch the pedals (especially for shorter people).
Solution: Play with your toes only and take a slower tempo.
4. Bench in historical organs too low. When the bench is too low and you can't change it's position, pedal playing requires a lot more muscle work.
Solution: Add additional wooden blocks or hymnals under either side of the bench.
5. Pedalboard too deep. When the organ has several manuals, sometimes reaching for the top manual and playing on the pedals is very uncomfortable - pedals seem too far away. And you can't move the bench closer because you will touch the lowest manual.
Solution: Don't play the most difficult parts of your piece on the top manual. If you do - slide forward to the edge of the bench.
6. Short octave in pedalboard. Some Baroque organs have an incomplete octave in the bass lacking the lowest accidentals. This layout makes it very easy to play the wrong notes by accident.
Solution: Find out the layout of the bottom octave ahead of time and pretend you have the same situation on your organ. Mark those notes on the score and practice them in advance.
7. Additional subsemitones in pedalboard. Similarly to the problem No. 6, some historical organs have additional keys for D#/Eb and/or G#/Ab (even in the pedals). This situation makes it quite strange to play chromatic music.
Solution: Same as No. 6.
Think about the above unusual problems and if you have the privilege to play such organs, you might avoid those pitfalls, if you prepare in advance in your mind.