Got the xml. It’s as I thought.
guid=“com.plexapp.agents.none://?lang=xn”
Your video has this as it’s identifier. Which is wrong. There should be something after those 2 slashes. Something is wrong so that the identifier is not being created properly. So your server is not actually merging the 2 videos, it’s creating the same messed up identifier which coincidentally causes them to be treated as merged videos.
It’s something specific with those 2 files causing the bad identifier.
You can try a Plex Dance on those 2 files to see if it will fix the identifier. I have a guess as to why this is happening and will bring it up with the team.