Hi darksen
Yes such playlists are "bad", because in the first (and/or last) m2ts is a video stream only.
You can ignore such m2ts files. When you load such a playlist in BD2mkv you have the option to ignore the m2ts files.
cE can ignore such m2ts files automatically: in the settings yon can set a duration for such files.
Mostly is the duration less then a second. The default duration is 2 seconds.
I'm not sure if mkvmerge can handle such playlist correctly.
It would be nice if you can share with me a chunk of this disc. You can use my
DiscShare tool.