Continuity mistake: When Lawrence is watching the Weeping Angel, just after seeing the Doctor's film/Easter egg, he turns away for a split second. By the time he turns back, you see the Weeping Angel's face only inches from Lawrence's face. But you then cut to a wide shot where you see the Angel's arms outstretched, so its face is about half a metre away from Lawrence's face. (00:34:45)
Continuity mistake: When Mr. Copper is talking about how space-lane fraud could get him ten years in jail, the cut on his forehead changes sides, as does the panel behind him, revealing the shot to be flipped. (00:36:25)
Evolution of the Daleks (2) - S3-E5
Revealing mistake: When Dalek Sec picks up the remains of the radio and turns it in his hands, the "Hamilton" label on the front of the radio is written backwards, indicating that the shot has been flipped horizontally. (00:05:00)
The Sound of Drums (2) - S3-E12
Continuity mistake: When gassing the cabinet members, the Master puts on a gas mask. The Valiant logo is above the tube, and upside down. In the next shot, it is below the tube, and the right way up. (00:04:50)
Evolution of the Daleks (2) - S3-E5
Continuity mistake: When Martha is searching for how the Daleks changed the design of the Empire State Building, she is examining the plans for the top of the tower. In the first shot where the new plans are visible, the upper right shows a more detailed picture of a plate of Dalekanium. Seconds later, when we can see the new plans again, it's the same side view but the enlarged picture of the plate with the Dalek bumps is gone. These are still the same new plans (the old plans are on her right) and there was no time or reason for Martha to take another page. (00:24:40)
Visible crew/equipment: As Sally enters the living room in the abandoned house, in the shot where she walks through the doorway, a cameraman holding the camera can be seen reflected in the window of the door next to her. (00:00:35)
The Family of Blood (2) - S3-E9
Continuity mistake: When Sister of Mine enters the school's courtyard after the battle with the scarecrows, her right hand is holding her balloon at the bottom, with the bottom of the string wrapped around her left hand. In the next shot, facing her, her right hand is at her side, with the balloon floating above her left hand. The balloon proceeds to jump between positions until Sister of Mine murders the headmaster. (00:18:00)
Daleks in Manhattan (1) - S3-E4
Continuity mistake: When the Doctor turns the newspaper towards Martha so she can read the headline, in the wide shot, the corner in his right hand is bent back towards him. In the close-up showing the headline, the corner is straightened with his hand in a different position. (00:04:29)
Continuity mistake: When the Doctor starts scanning Korwin, he's holding the sonic screwdriver with his thumb on the end without the light. When Ashton says that Korwin sabotaged the ship, the Doctor's grip on the screwdriver has changed to one without his thumb on the end. Shortly after, he has his thumb on the end again. (00:06:10)
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)
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)
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)
Continuity mistake: When the Doctor interrupts Mr. Copper's incredibly inaccurate description of Earth society to ask him where he got his information from, in a shot facing Mr. Copper, the Doctor's raised hand has only one finger extended. In the next shot, facing the Doctor, he has two fingers extended, with the other two only loosely curled. Shortly after this, the Doctor scratches his temple with that same hand, only for it to be absent in the next shot facing Mr. Copper. (00:11:40)
Continuity mistake: After Milo and Cheen abduct Martha, they put a sleep patch on her before entering their car. In the close-up where Cheen applies the patch, it's stuck on securely and neatly, with the top and bottom of the square pointing directly at Martha's head and chest respectively. In a wide shot immediately afterwards, the patch is stuck on quite loosely and has gone askew. (00:06:35)
Continuity mistake: When the Doctor and Martha open the doors to the balcony, in a shot facing them, Martha lets go of the handle of her door and it swings completely open. In the next shot, from behind, Martha is still holding the doorknob. (00:10:35)
Continuity mistake: When the Doctor is looking out the window while asking Martha if there's a balcony on the floor of the hospital they're on, in close-ups of him only his right hand is visible, resting on the sill between two windowpanes, and his left arm is by his side. In a wide shot from outside looking in, his left arm is stretched out with his left hand gripping the divider between two windowpanes, in a spot where it should have been visible in the preceding shot. (00:10:05)
The Family of Blood (2) - S3-E9
Continuity mistake: When Martha finishes listing off the bones of the hand to Joan, in order to prove that she's a medical student from the future, in a shot facing Joan, Martha's thumb is extended. In the next shot, facing Martha, her thumb is suddenly folded back, as if she was using her hand to display the number 4. (00:12:15)
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.