I use Seriesguide and Trakt from a long time now, they always worked great, but in the last few months a problem showed up. For animes it gets wrong watched status from Trakt, like: Bleach, Dragon Ball Super, Naruto Shippuuden, Sket Dance, The Melancholy of Haruhi Suzumiya. Even if the show is fully watched in Trakt, the app says that only some few episodes were watched; it even shows that the show has only one season (that happend for Dragon Ball Super and Bleach). I did’t see this behavior with tv shows that are not anime.
I unninstalled the app, cleared the data, remade the connection with Trakt a few times and the problem persists.
Since SeriesGuide has already completely switched to TMDB for show data, it may not match with what is on Trakt. E.g. the season and number of an episode might be different. It will require Trakt to fix those shows to use TMDB data as well. You can report the affected shows to Trakt on their Trakt site (look in the left sidebar for a report button).
Just reporting the show on Trakt will not change anything if the comparison between TVDb and TMDb is not 100% the same.
In order for Trakt to be “fixed” then the show data on TVDb and on TMDb needs to match, only then will Trakt fully switch that show to view TMDb as the data to follow.
You can add/change/update TMDb if you are sure the data you are changing is correct.