Give a man a fish/teach a man to fish...
With any disc there could be a dozen reasons for this:
Opening title and/or end credit on-screen text in different languages; different versions of the same movie/show (Director's Cut/Extended/Unrated/etc.); different distributor logos in different countries; foreign voice actor credits appended (shown/not shown depending on the language selected on the player); obfuscation (dummy playlists); picture-in-picture playlists (note that MakeMKV still (as of V1.17.3) hides any subsequent video tracks so you may not know they even exist unless you inspect the decrypted files yourself); sometimes commentary tracks are in a separate playlist; sometimes with different chapter editions; and a lot of times Japanese languages are in a playlist file all by themselves (if you want to know why, ask Universal Pictures and let me know
).
Just to name a few.
To begin with, I play every disc firstly in my regular LG home Blu-ray player and map out all the contents in a text file. Noting down the track title, duration, chapter count, chapter names, and sometimes the first line of dialogue if there are multiple tracks with identical runtimes (like "Previously on...").
Once I have a good idea of what's on the disc, I make a decrypted backup (I keep these, but you can obviously delete it again afterward if you're tight on storage space). The reason I like to work from a decrypted backup is that I can play a transport stream (*.m2ts) directly from the decrypted backup folder using VLC Media Player if I need to confirm something prior to ripping the files to .mkv
You might say that's 'double-handling', but the time it takes to rip files from a backup is far less than direct from an optical drive, and a lot of times I end up ripping a file more than once (often I need to rip, then extract the subtitles to examine/identify/label/order them properly, then rip again), so ripping speed is even more important.
Plus, as mentioned, this means I have a copy I can open again in MakeMKV any time in the future, or even play directly (menus and all) with VLC MP.
Getting back to playlist identification... As @dcoke22 said, the segment map provides a huge clue here.
If one playlist has an different/extra segment, you can go to your decrypted backup "STREAMS" folder and play that particular segment, which will show you what the difference is with that playlist.
If all your playlists have identical segment maps then the difference will be within the playlist itself. Some playlists pick 'n choose which tracks to include (like the commentary or Japanese language tracks mentioned above). Some may have different chapters, some may have picture-in-picture tracks hidden by MakeMKV so they may seem indistinguishable from the primary playlist.
If it's deliberate obfuscation then there could be hundreds of fake playlists (I think it was Lionsgate that was doing this for a while). Somewhere within the coding of the disc menu is an instruction for your regular player to choose the correct playlist, but we don't get access to that information, so your best shot is to find out whether anyone has dealt with that particular disc/title before. There will often be a thread here where somebody has already figured out which playlist is the one you want.
If all that fails and you still can't find a difference between multiple playlists then maybe it just doesn't matter, pick one and move on!
. I'll stick with the 16 chapter version, and load up the UB820 if I want to watch anything else. Thanks both for your advice 
.