During our last Unda Maris studio practice session at Vilnius University, I observed a student play Brahms's chorale prelude "Herzlich tut mich verlangen" (this is a video played by Thibaut Duret, organ by Michel-Merklin-Kuhn de St Louis de la Guillotière, Lyon, France).
What struck me the most was that his fingers often were holding several keys at a time (especially the top notes of the arpeggio). The result was quite messy.
I told him about this but it wasn't an easy fix.
Apparently his fingers aren't strong and independent enough to play clearly their own melodic line.
If you are in a similar situation, I recommend you strengthen your finger independence by practicing special exercises, such as from Vidas' Left Hand Training regularly. Play it with your right hand too in alternation. Then the technique of both hands will become stronger.