If you're sure the extra stuff is really on the disc, it could be referenced in the skipped .mpls titles that MakeMKV is discarding because it thinks the .mpls is a duplicate.
View Skipped Titles?
If you make a decrypted backup of the disc then delete the .mpls file that MakeMKV is choosing, it'll force MakeMKV to choose the other .mpls when you open the modified backup in MakeMKV.
Alternatively, you can use
MKVToolNix and open the index.bdmv file from a decrypted backup and potentially create a .mkv file from the skipped .mpls file.
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Here's a little background. The .mpls files on a blu-ray can be thought of as a playlist. The files that actually contain the audio and video are
.m2ts files. A .mpls file is a playlist of .m2ts files. (This is a bit of an oversimplification…)
If you make a decrypted backup of a disc, MakeMKV copies the contents of the disc to your storage, replicating the
blu-ray's folder structure. Inside that folder you'll find a BDMV folder and inside there will be a STREAM folder. Inside the STREAM folder will be a bunch of files named #####.m2ts where the ##### is 5 numbers. You can play these files with
VLC or several other players.
In MakeMKV, if you open the disc (as opposed to making a backup) and highlight a title on the left, you'll see a bunch of details in the 'Info' box on the right. The 'Source file name' will be the .mpls file the title references (if there is one at all). The 'Segment map' will be a list of numbers. Those numbers are the filenames of the .m2ts files with their leading zeros stripped away. For example, a segment map entry of 245 will correspond to file 00245.m2ts in the STREAM folder. A segment map of 245, 43, 234 means those 3 .m2ts files will be played, in that order, seamlessly by the player (this is called seamless branching).