2 different movies but considered duplicate of 1 movie how you fix?

I was able to match the first one manually with The TMDB agent.
The second one did not match, there was only the 2006 movie as a hit. Which is explainable, since the second edition is not listed on TMDB. They have only the original and the ‘final cut’ version.

I was able to include the second version as a ‘local extra’ of the first one.

/ Movies
   / Loose Change (2005) - (tt3029910)
      Loose Change (2005) - (tt3029910).mkv
      Second Edition-featurette.mkv

The only explanation I have why you couldn’t even match the first one correctly is that you made some mistake during the Plex Dance
It must be performed exactly as written: all steps in the right order. And only if Plex server is not still busy doing other things, particularly not while it’s updating libraries or metadata.