Okay, the issue is actually that there was the same bug in Discogs, setting the DiscNo to not alter on the Preferences/Remote/Discogs tab has no effect, instead it uses the value of Preferences/Remote/Discogs/TrackTotal.
So when you do Update from Musicbrainz and there is also a link to a Discogs release the problems occur.
Two possible workarounds:
1. Set Preferences/Musicbrainz/AutoMatch/Do not update from Discogs when Matching
2. Set Preferences/Preferences/Remote/Discogs/Track Total to Do not Alter