Most likely your plex TV agent advanced settings is using the TV Episode ordering from TMDB Bungo Stray Dogs: Season 1 (2016) — The Movie Database (TMDB) which has this show listed as one season rather than 3.
You can fix this by 1) renaming the files to match TMDB or 2) by editing the show itself in plex and changing the episode ordering in the advanced settings to match your naming of the files, TheTVDB (Aired) or TheTVDB (DVD) – I suspect DVD based on your naming above.
