Before I answer this question, if you are not sure what cadence is, let me briefly explain it to you. A cadence is a harmonic or melodic idea which helps to bring a musical section to a close.
So if you imagine this chorale prelude, a good place for cadence is the end of the opening episode, called Ritornello. It repeats in various ways throughout the piece and serves as a nice connection between the appearances of the chorale tune.
In order to answer the question of cadences and why they are difficult to master in this composition, let's look at the harmonic rhythm of this piece. For people who are not sure what "harmonic rhythm" is, let's just say that it refers to the frequency of how often the chords or the harmony change throughout the piece.
If you look at the pedal part, which is the basis of harmony, you will notice that the chords and the harmony in this chorale prelude usually change twice per measure, that is every two quarter notes. Here I don't mean the simple inversions of the same chord or non-chordal tones which might change more frequently.
If the harmony usually changes every two beats, the places when it changes a lot more frequently are the cadences. In a typical cadence of this piece, the chords usually change every beat or even every eighth note.
It is precisely because of this frequent changes of chords and a denser texture that the cadences are more difficult to master in this piece. You see, quicker rhythms require a better hand and feet coordination from an organist. Therefore the process of learning the piece is slower here.
I recommend learning the cadences in a slow tempo: hands and feet separately, then combinations of two voices, and only then the entire three-part texture.
By the way, if you like chorale prelude "Wachet auf, ruft uns die Stimme", BWV 645 by Bach , check out my brand new BWV 645 Home Study Course in which I will teach you how to master this piece in 17 days or less while practicing only about 30 minutes a day!
To your success in Bach organ playing,