maybe she did go back to work with Dante later, that's the only explanation anyway, even though the way they said everything implied that ever since the Mallet Island incident, she's been working with him, but it works the other way around too.
anyway, I know its canon, its not less canon than the games, but the games are more canon than the anime. the difference is, the games have higher priority over the anime, I really don't think if they contradict each other, they'd use the anime as the true information & use it on a sequel & disregard the games.
the big contradiction is Trish being Dante's partner, it can be solved as "Trish went back to work for Dante", other things aren't in your face, like Lady paying Dante less because Trish made the situation worse, I could translate it in a different way, she didn't pay Dante less because Trish did that, she only said that after Trish complained not because Trish complained. its weird to take her words that way, but I'll take 'em if it means more consistency.
anyway, the mangas aren't canon, they went out of their way when they said the anime was canon, the word canon was on every sentence that mention the anime. yet not a single word was out about whether the manga was canon or not.