OK, you have a subfolder inserted which is stirring up the matching process.
/volume2/TV Shows/Marvel/Marvel's Agent Carter/Season 1/Marvel's Agent Carter - S01E01 - Now Is Not the End.mkv
You must not insert additional subfolders. Only Show Titleand Season 0x folders.
Get rid of the Marvel subfolder.
Then perform the Plex Dance with all shows which were previously situated within this subfolder.
