Plex merging the wrong series

FYI, perform an Empty Trash before you Clean Bundles (Plex Dance).

When you put the series back into Plex, add them one at a time. Let Plex finish sorting, adding metadata, etc for the first before adding the second.

If you continue to have issues, try adding a season folder and renaming the files (followed by a Plex Dance). Delete the DVDRip… type info from the file name or put it in square brackets so Plex will ignore it.

/A TV Library
  /Salem
    /Season 01
      /Salem - s01e01.mkv
      /Salem.s01e02.[DVDRip....].mkv  <-- square brackets for other info you may wish to keep.
      /Salem s01e03 [DVDRip....].mkv 

Plex Docs -> Your Media -> TV Show Files (Naming and Organizing)