The Sontaran Stratagem (1) - S4-E4
Continuity mistake: When Private Harris orders the two hypnotized workers in the basement of the ATMOS factory to let him through the door they're guarding, he's holding a torch in his left hand, and when shown from behind has that hand down by his side. In the Sontarans' video feed, which also shows him from behind, his left hand is on his assault rifle. (00:11:15)
The Sontaran Stratagem (1) - S4-E4
Continuity mistake: When General Staal surprises Privates Harris and Grey in the room with the cloning tank beneath the ATMOS factory, the position of his right hand, holding his command baton, changes between shots several times. (00:14:10)
The Sontaran Stratagem (1) - S4-E4
Continuity mistake: When Martha asks the Doctor to look at her so she can point out she's not carrying a gun, he's sonicing an ATMOS device, and he lowers his hand when she speaks. In the next shot facing Martha, the Doctor's hand is raised again. (00:16:10)
The Sontaran Stratagem (1) - S4-E4
Continuity mistake: When the Doctor gets embarrassed as Donna lightly mocks him for not realizing that when she said she wanted to go home, she only meant for a brief visit, he rubs his chin with his left hand. When Ross Jenkins interrupts by saying, "Ready when you are, sir," the Doctor is now rubbing his chin with his right hand. In the shot after that, it's back to his left hand. (00:20:40)
Continuity mistake: When the Doctor opens a shipping container full of Ood and he and Donna stand in the entryway, he only opens the right-hand door, leaving the other one shut. In a shot from behind the two of them, facing into the crate, the left-hand door is now wide open. (00:17:15)
Continuity mistake: When the Doctor and Donna enter Warehouse 15 and see the Ood Brain, the Doctor rests his hands on the railing with his right hand off to his side. In shots from above and behind him and Donna, his right hand is closer to him. (00:35:30)
Continuity mistake: When Ood Sigma steps in front of Mr. Halpen while he's holding the Doctor and Donna at gunpoint and suggests he have a drink, the glass Sigma holds up is empty, despite the fact that he was heard pouring Halpen's tonic into it just moments before. In a shot later in the scene, the glass is shown full. (00:37:30)
Continuity mistake: For most of the scene where the Doctor and Donna find the dying Ood Delta-50, the front of his body is covered in snow. After he mentions "the circle", when the Doctor is asking what that is, the snow on Delta-50's chest is gone. In addition, the Doctor's hands change position between shots. (00:06:25)
Continuity mistake: During the first scene in Warehouse 15, when Dr. Ryder puts his hands on the railing as he looks over it, the exact positioning of his right hand changes between shots. (00:15:05)
Continuity mistake: When the Sybilline priestesses kneel after the High Priestess speaks, in a shot from the front, Donna, sitting on the altar, has her hands in front of her - she's using her left hand to take the rope off her right wrist. In the next shot, from behind, her hands are at her sides. In addition, the rope still on her right wrist disappears. (00:27:05)
Continuity mistake: When the Doctor explains to Donna how he sees the universe, the distance between them changes several times. (00:31:40)
Continuity mistake: When the Doctor is talking to Evelina at the end, her hair changes position between shots. (00:44:00)
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)
Continuity mistake: After Metella hands Caecilius the beetle brooch, his hands change position between the close-up and the wide shot. (00:46:10)
Continuity mistake: When the Doctor and Donna are talking to Caecilius, when they introduce themselves as "Spartacus" and Caecilius makes several guesses as to their relationship, wondering if they're married or siblings, in shots facing them, the Doctor and Donna are standing fairly close together. In shots facing Caecilius, however, the Doctor and Donna are standing much further apart. (00:11:05)
Continuity mistake: After Lucius' arrival, when the Doctor escorts Donna towards the TARDIS, telling her they have to go, which she doesn't agree with, between shots his hands change position between having his right hand on her back, or having both his hands on her shoulders. (00:13:55)
Continuity mistake: When the Doctor and Caecilius are talking while the Doctor examines the hypocaust, Caecilius keeps changing position. (00:17:40)
Continuity mistake: In Lucius' house, when the Doctor pulls the cloth off the shelf with the stone circuits, the position of Quintus' hand on the shaft of the torch he's holding changes between shots. (00:19:10)
Continuity mistake: When Donna changes into contemporary clothing, she has a purple shawl of sorts draped over her dress. In the first shot, she's shown with her hand out from under the cloth, but in the next shot her hand is under the cloth. (00:19:30)
Continuity mistake: When Ms. Foster's computer switches back on because it's picking up a signal from the Adiposian First Family, in a shot facing him, the Doctor reaches towards it with his left hand. In the next shot, from behind him and Donna, his left hand is resting on the wall next to the computer, before he reaches for it again. (00:39:25)
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.