I'm not sure about this, but I'm listening to the "Gothic 2" Soundtrack right now and in the track "The Monastery Surface" are a few "Clicks" - I don't think they belong to the music. Or is it just a corrupted file on my my computer?

I have them as well. They sound like recording artifacts to me.

I can't really remember, but I think that in-game monastery music had the same problem (I don't have the GOG version so I can't compare it).

Something I should have confirmed a few years ago but yes, the monastery chapel music gets corrupted while playing the game and GOG ripped the corrupted file. Reinstalling the game restores the original music which doesn't have clicks and is completely different.