9. Clara's Fractures
Poor Clara. For the majority of her time alongside the Eleventh Doctor, she's no more than a walking plot device. More focus is put on the mystery behind her recurring appearances at different points in time than on her actual character. With so much build-up there needed to be a satisfying payoff, and while the answer to this mystery was a clever one, it was also a pretty big retcon.
Clara stepped into the Doctor's timestream in an effort to save him from the Great Intelligence, scattering versions of herself across his timeline. With some smart reuse of archival footage, Clara appears to cross paths with many of the Doctor's past incarnations in familiar episodes: the Tenth Doctor in Silence in the Library, the Seventh Doctor in Dragonfire, the Fifth Doctor in Arc of Infinity, effectively retconning these stories so that Clara was always present in them, we just never saw her.
Most egregiously however, we see Clara converse with the First Doctor himself, just as he is about to steal a TARDIS and leave Gallifrey behind. Clara calls out to the Doctor and persuades him to take a specific TARDIS, thereby ensuring that he ends up with the notoriously unreliable time ship we all know and love. This retcon attempts to amplify Clara's importance to the mythos by implying that without her, Doctor Who as we know it would never have existed.