Continuity mistake: When Clara draws the Doctor's attention to the vision of a forest appearing in the archway, the candelabra she is holding has two candles in it, with the third hole empty. Moments later, after the apparition has disappeared, there are now three candles in it. (00:15:30)
The Parting of the Ways (2) - S1-E13
Continuity mistake: At the beginning of the scene where Rose, Jackie and Mickey are in the restaurant, in the wide shot, Rose moves her left hand to the side of her head, while looking down with her head facing towards the other side of the table, which her elbow is resting on. In a close-up immediately afterwards, she's looking out the window with her hand to her face and her elbow resting on the windowsill. (00:18:50)
The End of Time: Part Two - S4-E18
Continuity mistake: When Wilf looks down while holding his service revolver at the end of his conversation with the Woman in White, the position of his right index finger changes between shots. (00:23:35)
Continuity mistake: As the Doctor stares down at young Amy, he takes a perfectly red apple from her and bites it. When the angle changes, and he spits the bite out, the apple has changed to an ordinary red and green one. (00:06:05)
Continuity mistake: After the Doctor and Wilf get off the seniors' bus, they're waving goodbye. In a close-up shot, the Doctor is waving with his right hand, but in a wider shot immediately afterwards, he's switched to his left hand. (00:25:10)
Continuity mistake: When Bonnie is filming the transformation of the Zygon man who she stripped of control over his shape, her grip on the phone she's using changes between shots.
Continuity mistake: When the Captain's arrival at the South Pole is first shown, walking up while Twelve is explaining to One that the frozen snow means something is very wrong with time and asking if either of them is a doctor, to which Twelve responds, "You trying to be funny?", the two Doctors are standing right next to each other. When the Captain's arrival is shown from his perspective, however, the Doctors are standing much further apart when Twelve says the line. (00:09:00)
Continuity mistake: When Sally takes out the list of DVDs while talking to Billy in the hospital, her grip on the paper changes between shots. (00:25:40)
Mummy on the Orient Express - S8-E8
Continuity mistake: When the Doctor phones Clara and discovers she's trapped in the locked car with Maisie, his phone keeps switching hands. (00:21:55)
Continuity mistake: After the Doctor gets directions to the motorway, when the red-haired female pharmacist leans over her counter to try and persuade him to buy some Happy, her hands change position between shots. (00:08:00)
Continuity mistake: When the Doctor first enters Shakespeare's room at the inn, the collar of his coat is askew. The scene cuts to Shakespeare, and when it cuts back to the Doctor his collar is now flat, without him having moved his hands from his pockets. (00:09:20)
Visible crew/equipment: After the acting Prime Minister gives orders to the sergeant and the lift doors close, the soldier turns around. As he issues orders, the boom mike is reflected on his goggles. (00:05:25)
Silence in the Library (1) - S4-E8
Continuity mistake: When the girl recognizes the Doctor on her TV, telling him that he was in her library, and he reacts, the position of her pencil crayon in her hand changes between shots. (00:20:45)
Last of the Time Lords (3) - S3-E13
Continuity mistake: When Martha explains to Tom and Professor Docherty about how the Master could only use the TARDIS to travel between the present day and the end of the universe, and how he must have gone to Utopia, in a wide shot her right hand is resting on the table, but in a shot from above looking down on the captured Toclafane her right arm is by her side. (00:20:15)
The Sound of Drums (2) - S3-E12
Continuity mistake: After the Master calls Winters "the last President of America", in a shot from behind him and Lucy, he has his hands by his sides. In the next shot, facing them, the Master has his hands clasped behind him. (00:31:35)
The Lazarus Experiment - S3-E6
Continuity mistake: After Lazarus emerges from the pod, when he announces himself to the crowd, in a wide shot, his arms are lowered, but in a close-up immediately afterwards his arms are raised. (00:09:15)
Forest of the Dead (2) - S4-E9
Continuity mistake: After the Doctor tints Anita's visor, as he explains to River that he did it to try and trick the Vashta Nerada into thinking they're already inside Anita's suit, the position of his right hand, holding the sonic screwdriver, and the fingers of that hand change position between shots. (00:10:25)
Continuity mistake: When the Doctor picks up a skull from the bones waiting to be ground into fertilizer, the position of his hands holding it changes between shots facing him and shots looking at the skull. (00:15:10)
Continuity mistake: When the Doctor starts scanning the wall of the tunnel as Jenny asks him who he is and if he's an anomaly as well, his grip on the sonic screwdriver changes between shots. (00:22:20)
Continuity mistake: When the Doctor and Donna leave as Caecilius, Metella, Evelina and Quintus stand and watch the destruction of Pompeii, the TARDIS changes orientation between shots - in both of them, one from in front of the family and one from behind, the TARDIS' door, with the sign, is visible. (00:45:10)
Chosen answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.