The Toccata and Fugue in F Major for organ (BWV 540) are believed to be two separate entities that Bach joined together to create a single work. The Toccata was probably composed during his Weimar years; the Fugue was composed later during Bach’s tenure in Leipzig.
If these assumptions are correct, it means that Bach wrote the Toccata for one instrument and the Fugue for another. In Bach’s day, as today, organs varied greatly from one to another. This is yet another instance of Bach at his creative best.