It's not easy to hear, I must admit. I had to play the Fagius from disc, at a slower speed.
First, I'm just a layman, so this could be a wild guess: could it be an adornment, in the shape of a broken chord (he suggested very hesitantly)?
Well, the last assumption might be .... not entirely true.
From what I know, there are differences in the E and C major versions, probably because of the size and range differences of the various keyboards.
Also, there are no original Bach manuscripts of BWV 566, but only various copies by others (mainly pupils of Bach) of both versions, probably with slight differences. This is quite often the case in the Bach organ catalogue.
Sometimes these differences are caused by mistakes by copiists, sometimes because of the earlier mentioned different instruments that the copiists played themselves, with different keyboard or pedal range for instance.
So, what version do the various organists nowadays prefer to use?
Johann Tobias Krebs, Johann Christian Kittel, Johann Kirnberger, Christian Friedrich Gottlieb Schwenke?