Doctor Who as a whole has never had an official "canon", which means that there is nothing to force the continuities of different ranges of spin-off material to match up. As far as most publishers care, as long as the story is consistent within their own range, that's enough. The Eighth Doctor's timeline is notoriously complicated because of this lack of need of consistent continuity between ranges, although some stories have tried to reconcile the various continuities together. You also must remember that there is even a lot of contradiction within individual ranges of Whoniverse stories, including the TV series. The best way to explain this away in-universe is that time is in flux and history can change, and in fact that is usually the excuse given in stories, such as in "Good Night".