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.