
First of all, let me warn you this Blu-ray disc was decrypted using AnyDVD-HD, but AnyDVD is never enabled here when I see this warning.
Second, I have tested a few decrypted folders (from other Blu-ray discs and different companies) and this message usually appears not when there's something wrong with the decrypted files. In fact, there is NOTHING WRONG with them.
Third, let me quote you an example of movie with this issue: Predator 2 (1990).
This movie has a DTS-HD MA 5.1 and DD 2.0 track for the movie. And also, 2 Audio commentary tracks.
However my copy doesn't have a DD 2.0 track, but portuguese instead. It's a disc from Brazil. This is not an isolated case, I have seen this problem happening several times with discs from US and other regions as well.
I have seen this happening when the disc has a certain number of audio/subtitle tracks and/or when the disc is authored in a different way.
For the record, I have used these softwares to perform my tests:
TotalMedia Theatre 5 from Arcsoft, to open the BDMV folder;
tsMuxerGUI, freeware, available here:
http://www.videohelp.com/tools/tsMuxeR
When this problem happens, we might proceed with MakeMKV, however I have seen (and again, in more than a single case) the program crashing (freezing) after at least 50% it's completed. So we are advised to not proceed.
Analysing this particular disc in MakeMKV (going forward), I saw this data (note: I have opened the index.bdmv file):


As you can see, the movie is listed twice. In the second time, you will see additional japanese subtitles, that are not available to be selected in the other "title". By the way, this movie has no additional versions or angles.
Now we are going to use TMT from Arcsoft.
But wait: if we select any other language (rather than JAPANESE) for the menus, we will only see those first options from MakeMKV. If we select (in TMT settings) the JAPANESE language, we will see these additional languages (3 JPN).
And now, let's open the 00013.m2ts file (33 GB) from the BDMV folder, using tSMuxerGUI:


Now, using TMT with Japanese language for menus (while watching the movie):
Subtitles > Japanese
Subtitles > English
Subtitles > Japanese
Subtitles > Japanese
Subtitles > Japanese
English/(or any other language) for menus (while watching the movie):
Subtitles > English
Subtitles > Portuguese
Subtitles > Portuguese
Subtitles > Chinese
Subtitles > Korean
Subtitles > Korean
Subtitles > Korean
Subtitles > Spanish
Subtitles > Spanish
Subtitles > Chinese
Subtitles > Thai
Subtitles > Thai
Now using Media Player Classic-Home Cinema, to open the 00013.m2ts file (33 GB) from the BDMV folder:

AS you can see, the whole thing is scrambled.
But I have identified, using MPC, what are the subtitles available for the whole thing.
Movie = It has english and portuguese subtitles. The second portuguese subtitle is Text-only, which means that kind of subtitle that is only used for 4, 5 scenes even if the movie has 2 hours. So, we have 3 subtitles that I want here. The rest (in other languages) is exactly this: Movie and movie-text-only.
Audio commentaries: there are 2, however the only language they are available is japanese/korean.
1st Audio commentary = korean subtitle 2
1st Audio commentary = japanese subtitle 2
2nd Audio commentary = korean subtitle 3
2nd Audio commentary = japanese subtitle 3
How do I know this? It's simple, switching subtitles using MPC or even TMT.
And apparently, TsMuxer's second subtitle (PGS, Chinese) is the english one, since it is not listing English.
I am explaining all this, in order to help you (in case you are not aware about everything I explained) how to identify this issue. I wonder if this method of authoring Blu-ray discs is responsible for confusing MakeMKV and sending this warning to us. I don't like using TsMuxer for this, and it would be great if MakeMKV let us unselect the second title's video from that list.
I would have to convert to Matroska this movie twice to extract the japanese subtitles.