Hello,
I'm not quite sure if it is metadata or what but I have a few movies that have additional movies. I think it was Iron Man 3 that came with Agent Carter about Cap's girlfriend after his plane went down. It is about a 15 minute short. When I turned it to an MKV the name of the MKV file is Agent carter but my Oppo sees it as Iron Man 3 (twice) and only plays the full movie, not the agent carter short. I have to put it in a different folder than Iron Man 3 and then Agent carter plays fine.