The problem I'm running into is MakeMKV sometimes doesn't see, and therefore doesn't rip, all content on a disc - usually extra chapters on a title.
I've run into this before, but the current example I'm dealing with is the Planet Earth (original, not II) blu-ray. All of the episodes have an additional 'Planet Earth Diaries' segment at the end, but this segment doesn't show up in any of the ripped titles.
The only errors I'm seeing in the log are AVSync that seem to be talking about audio/subtitle tracks, but not entire missing chapters:
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AV sync issue in stream 2 at 0:00:00 : Track #2 turned out to be empty and was removed from output file
AV sync issue in stream 3 at 0:00:00 : Forced subtitles track #3 turned out to be empty and was removed from output file