Its actually good that you did the Witchwood quest
before the Hydra quest, because you otherwise would have failed it, and completely missed out on the Witchwood storyline. Dragon's Dogma is the one game I absolutely encourage people to play with some kind of guide, because there are plenty of situations like this. The game world moves through what are commonly called "stages" by the fans, with new stages triggered by completing certain main lines quest or starting a particular quest. And if you move from one stage to the a stage without completing certain quests from the previous stage, those quests will automatically fail, and the game
doesn't specify this or tell you which quests are time sensitive. I highly recommend keeping the
game walkthrough on hand, particularly the parts on
story progression stages and the
side quest start and fail points, just so that you can keep track of which quests will fail at which times, so that you know what absolutely has to be completely first.