FileBot

Example: Skipped [/Users/richard/CompletedDownloads/Major.Crimes.S06E09.HDTV.x264-SVA[eztv].mkv] because [/Users/richard/Videos/TV Shows/Major Crimes/Season 06/Major Crimes - S06E09 - Conspiracy Theory - Part 4.mkv] already exists

The file Major Crimes S06E09 is not in the CompletedDownloads folder, but it is in my Plex library.

Why is this happening?

The exact text in the amc.log is:

Skipped [/Users/richard/CompletedDownloads/Vikings.S05E05.HDTV.x264-SVA[eztv].mkv] because [/Users/richard/Videos/TV Shows/Vikings/Season 05/Vikings - S05E05 - The Prisoner.mkv] already exists

Vikings.S05E05 is not in the Completed Downloads foler

Yes it is. According to the log. The original path exists, and it's not processed because the destination path already exists as well.