Continuity mistake: After the scribble creature has been analyzed and found to be made of graphite, the Doctor takes out a pencil and erases some of it to confirm this. The next time the graphite ball is seen, the erased area is gone. (00:14:35)
Continuity mistake: When the Doctor takes a swipe out of a jar of jam in Trish's kitchen and sticks his finger in his mouth, he only has his index finger in his mouth. The scene cuts to Rose giving him a "WTF" look, and when it cuts back to the Doctor he suddenly has two fingers in his mouth. (00:21:15)
Continuity mistake: When Rose grabs the drawing of the Doctor and the TARDIS from Chloe, the upper right corner is bent over rather sharply. In the close-up of the picture as Rose tells the Doctor she'll find a way to get him out of there, the paper is now only slightly wrinkled. (00:30:15)
Continuity mistake: When the Isolus leaves Chloe, in the shot facing Chloe where it says goodbye, Chloe's hand is raised to the wall, where the two were drawing a picture of the Earth. In the wide shot where the Isolus leaves Chloe's mouth, her arm is lowered. In the next close-up of Chloe, when she says "Mum?", her arm is raised again. (00:36:05)
Factual error: The Police motorcycle in front of the Olympic runner is an S registration, meaning it was registered in 1998. The episode is set in 2012, and there is no way the Police would have such an old vehicle on active duty.
Factual error: The Olympic torch relay is presented as if there is only one runner carrying the torch through the entire city of London to the Olympic stadium to light the cauldron. Furthermore, when the torchbearer collapses, the TV announcer reacts as if it is now impossible to get the torch to the stadium, just before the Doctor steps in and picks it up. Any broadcast of any Olympic opening ceremonies would show that that's not how the torch relay has ever worked.
Continuity mistake: At the start when we see Rose on the bus, a bald man sits down on the seat behind her. However, when the camera is inside the bus, he is sitting two seats behind her, without enough time for him to move. (00:00:20)
Continuity mistake: When Rose presents her mother with the Bazoolium, she's holding it in her left hand. When the view switches to look at Jackie, it shifts to Rose's right hand and then immediately back to her left when the view restores to the original vantage point. (00:02:45)
Deliberate mistake: When the Doctor is watching news broadcasts from around the world about the ghosts, the newspeople from France, India and Japan should be heard speaking English because of the TARDIS' automatic translation. (00:05:55)
Character mistake: Dr Singh refers to "a single protozoa." "Protozoa" is the plural form. He ought to have said "a single protozoan." (00:08:05)
Continuity mistake: When Jackie enters the TARDIS and closes the door, it shuts completely - despite the fact that there's a cable running out the door to the device the Doctor set up to catch one of the ghosts. (00:12:45)
Continuity mistake: When Yvonne leads the Torchwood soldiers in a round of applause for the Doctor and he starts lowering his hands, he does it twice, once in a shot facing Yvonne and again in the next shot facing him. (00:18:35)
Continuity mistake: When Yvonne Hartman is showing the Doctor through Torchwood after leaving the TARDIS, she goes to push a door open into the main building with one hand, but when the camera cuts to them entering the building she pushes them open with two hands. (00:20:10)
Continuity mistake: When Yvonne is taking the Doctor and Jackie to the Sphere Room, there is a sign opposite the door that has the words "Torchwood Institute". In the next shot where you can see the corridor from inside the Sphere Chamber, the sign has disappeared. It reappears again when Rose is going into the Sphere Chamber, but this time it has directions to the Reception, Canteen and Lever Room as well as "Torchwood Institute". It also disappears again when you see the corridor from inside the Chamber. (00:23:30 - 00:31:45)
Continuity mistake: In the sphere room the Doctor briefs Yvonne and Rajesh on the void. As he sits down in front of them you see Jackie's feet start walking towards them but the next cut behind Yvonne and Rajesh facing the Doctor shows Jackie isn't there. (00:25:15)
Continuity mistake: When the Doctor uses his sonic screwdriver on the glass partition in the Torchwood Institute, cracks radiate out in a star pattern, meaning the glass will break into pointed shards. When it does break, it breaks into cubes, like safety glass. (00:29:30)
Character mistake: In an early scene with Yvonne Hartman, she says "We've just measured the ghosts' energy at 5000 gigawatts." There are at least two mistakes here: (1) watts are a unit of power, not of energy (that would be joules); (2) later on, when Hartman is showing the Magnaclamp to the Doctor, she refers to imperial tons and says "Torchwood refuses to go metric", but a gigawatt is a metric unit.
Continuity mistake: When the Sphere Chamber is first shown, there is a rolling staircase set up just below the Sphere. Rajesh Singh is shown climbing the staircase and nearly touching the Sphere. However, when the room is next seen, when Raj hears that the Doctor is coming and walks up to look at the Sphere again, the staircase has vanished. Later, when the Doctor and Jackie are shown into the room while Yvonne gives them the Torchwood tour, the staircase is still missing, and it's more obvious that it is no longer in the room. It does not reappear for the remainder of the two-parter.
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.