I'm having a problem similar to this with SegaCD games. They're structured like this:
Game(NTSC)(US)\
Game(NTSC)(US)[!].cue
Game(NTSC)(US)(Track 01 of 12)[!].iso
Game(NTSC)(US)(Track 02 of 12)[!].wav
etc
If I tell it not to merge duplicates, it creates an entry for every file. If I tell it to merge duplicates, it correctly creates one entry, but if I Play it, it tries to launch a random WAV file in RetroArch. If I pick a version and select the cue file, it works.