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)
The Sontaran Stratagem (1) - S4-E4
Continuity mistake: When Jo Nakashima says, "If you won't listen, I'll find someone else who will," she's holding her purse and bundle of papers in the crook of her left arm. When she opens the door of her car, the items have jumped to her right arm. (00:00:45)
The Sontaran Stratagem (1) - S4-E4
Continuity mistake: In the TARDIS as Donna navigates, the Doctor uses a hammer to help correct the trajectory, then rests it on his neck and shoulder. A second later, when the phone rings, his hand, holding the hammer, is suddenly much lower, below his waist level. (00:03:15)
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)
The Sontaran Stratagem (1) - S4-E4
Continuity mistake: When Ross makes his "round the bend" pun while turning the Jeep onto Rattigan Academy's drive, the road seen doesn't match up with what's shown on the GPS display. (00:26:20)
The Sontaran Stratagem (1) - S4-E4
Continuity mistake: When the clone Martha sits up in the tank, in a shot from behind her the umbilical cord is trailing down her back. In a shot facing her, it's draped over her shoulder, only to return to being down her back when she unplugs it. (00:35:20)
Continuity mistake: When the Doctor pulls out a TARDIS key to give to Donna, the exact position of the key in his hand changes between shots. (00:05:00)
Continuity mistake: When Colonel Mace confronts Commander Skorr, he raises his gun twice; once in one shot, and immediately after in the other. (00:30:30)
Continuity mistake: When the Doctor activates the teleport, Donna is onboard the Sontaran ship, holding a cell phone in her left hand. When she arrives in the basement of the ATMOS factory, she's holding the rubber mallet in her left hand, and her right hand is empty, with the phone nowhere to be seen. (00:32:40)
Continuity mistake: Near the end, when Luke teleports and switches places with the Doctor on the Sontaran ship, Luke catches the atmospheric converter's switch twice, once in the wide shot and then again in his POV. (00:40:25)
Continuity mistake: When Donna is sneaking around the Sontaran ship, she's carrying Martha's old phone, which she's using to stay in touch with the Doctor, and the rubber mallet from the TARDIS. There are times when one of the two objects, the phone more often, is missing from her hands with no explanation.
Continuity mistake: When they get out of the TARDIS at the beginning, Martha and Donna change positions relative to each other between shots. (00:00:55)
Continuity mistake: During the conversation where Donna gives Jenny her name, Jenny's ponytail keeps changing position between draped over her shoulder and hanging in the back. (00:06:55)
Continuity mistake: In the scene where Cobb is briefing his troops, the troops all have their guns, but in the other scene (after you see the Hath marching) the troops are receiving guns. (00:15:45)
Continuity mistake: When Donna suggests that she distract the next guard using her "womanly wiles", she flips her hair behind her shoulder. In the next shot, when the Doctor tells her to save her wiles for later, the hair has spontaneously moved to its former position. (00:19:35)
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.