As it currently stands, scrobbling with Plex simply grabs the season and episode number of a show and tries to match it with Trakt. For anime, this does not work sometimes, e.g. Jujutsu Kaisen being organized as 3 seasons on Plex, while it's only one season on Trakt.
Plex stores the IMDb, TheTVDB, and TMDB IDs of every episode or movie as a GUID in the MediaContainer XML file. You could instead use this to properly match the media with Trakt, that way the match is successful every time and is more accurate than just going based off of the season and episode number alone.