The Lazarus Experiment - S3-E6
Continuity mistake: When the Doctor and Martha get into Lazarus' machine, it's shown to be very cramped inside - when the Doctor crouches down to access the wiring and circuitry below a floor panel, his head is right next to the skirt of Martha's dress. However, after he tells Martha what he's doing to the capsule, when he notes that the transformed Lazarus is three times the size of his human form, the Doctor is further away from Martha. (00:29:25)
The Lazarus Experiment - S3-E6
Continuity mistake: After the Doctor and Martha get out of the capsule and walk up to the human Lazarus, lying on the floor, Martha says it's kind of pitiful, turning to look at the Doctor as she does so. In the next shot, facing the Doctor, Martha's head is still turned to look at Lazarus. (00:30:10)
The Lazarus Experiment - S3-E6
Continuity mistake: In the cathedral, when Lazarus says, "You're so sentimental, Doctor. Maybe you are older than you look," his blanket has jumped up to cover his left shoulder, which was previously bare. The blanket then changes position several more times. (00:34:50)
Continuity mistake: When the Doctor asks Captain McDonnell how many other crewmembers there are on board, he grabs her arms. After she tells him "three", the Doctor lets go of her as Scannell explains that the ship transports cargo across the galaxy. In the next shot, facing the Doctor, he's holding McDonnell's arms again. (00:03:00)
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 the Doctor comes up with the idea of using the generator to restart the ship's engines, in a close-up he's gesturing with his right hand, but in a wide shot is gesturing with his left. (00:10:15)
Continuity mistake: After McDonnell warns the crew that the possessed Korwin killed Abi, Ashton orders Erina to hurry up with the equipment she was sent to fetch, and she mutes the com before removing several pieces of equipment from a locker, holding them with her right hand and arm. When she closes the locker door, revealing Korwin, the equipment disappears. (00:15:20)
Continuity mistake: After Korwin cuts the power to the stasis pod, close-ups of the Doctor inside the pod show light still on in the pod. A shot from outside the pod, however, after McDonnell runs off to deal with Korwin, shows the inside as being dark. (00:35:25)
Continuity mistake: At the beginning, when the Doctor asks Martha if they saw her face, her hands change position, from grabbing his arms in a shot facing her to facing up in a shot with both of them. (00:00:10)
Continuity mistake: When the Doctor says, in response to Martha asking how the Family can follow them, "Stolen technology. They've got a Time Agent's vortex manipulator," in a close-up of his face he reaches with his left hand for a control on the console, but in a following shot of his hands, they're right next to each other. (00:00:25)
Continuity mistake: When Martha and Jenny are washing the floor, just as Hutchinson and Baines come along and tell them off for laughing, one of the lace ribbons on Martha's cap moves between hanging in the back in shots facing her and draped over her shoulder in shots facing the schoolboys. (00:04:15)
Continuity mistake: When Martha initially bursts into John Smith's study after hearing that he fell down the stairs, the door is mostly closed. When she runs back to the door to knock on it after Joan Redfern tells her off for bursting into a master's study unannounced, the door is open wider. (00:06:35)
Continuity mistake: During Joan's encounter with the Family's spaceship, when it shines a beam of green light at her, she shields herself by raising her right arm. It changes position between a wide shot and a close-up. (00:12:20)
Continuity mistake: After watching the Family's spaceship land, Jeremy Baines puts his hand on a tree stump as he walks around it to approach the ship. He does this twice, in two successive shots. (00:14:10)
Continuity mistake: When the Doctor fits the Chameleon Arch watch into the headset, his hands change position between shots. (00:20:15)
The Family of Blood (2) - S3-E9
Continuity mistake: As the scarecrow-soldiers advance on the school to do battle, the scene cuts to Sister of Mine, looking out from a school window. There is heavy rainfall outside. When we immediately cut back to the advancing scarecrows, it is a cold, clear night. (00:10:00)
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)
The Family of Blood (2) - S3-E9
Continuity mistake: When Timothy opens the watch into the girl's eyes, Jeremy Baines shouts "Time Lord", then a few seconds later; "What are we waiting for. Attack!" There is then a shot looking down on the scarecrows, Jeremy and Jenny. If you look closely at Jeremy Baines, it's a different actor playing him. (00:16:20)
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)
The Family of Blood (2) - S3-E9
Continuity mistake: When the Doctor comes back to the Cartwright house after imprisoning the Family, Joan walks over to the window and looks out, clasping her hands in front of her. In the next shot, when she asks the Doctor if it's done, her hands are suddenly by her sides, and she is shown clasping them again. (00:34:45)
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.