Please watch Getting Started #2 and read Manual Matching for details.
CLI:
If the file listing (or input argument order) aligns naturally with the episode list, then you can use -list -rename to rename files / episodes in linear order, bypassing automatic matching (and any potential mismatches caused by misleading file names) altogether.

e.g. Rename files and episodes in linear order:
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filebot -list --q Firefly --format {plex.name} -rename *.mp4
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filebot -list --q Alias --format {plex.name} --filter "s == 2" -rename *.mp4
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filebot -list --q "The Daily Show" --filter "airdate >= /2007-01-08/" -rename -r .
e.g. Rename a movie file by numeric ID:
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filebot -list --db TheMovieDB --q 19995 -rename *.mp4