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)
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.
Continuity mistake: After Pete tells the Doctor that Mickey went ahead because he wanted to find Rose, the Doctor asks him if he knows that Rose is his daughter from a parallel universe. The problem is that in Pete's last scene in "The Age of Steel", the Doctor saw Rose call Pete "Dad", leading to Pete departing in a hurry. (00:15:05)
Continuity mistake: When Rose is hanging onto the lever and beginning to lose her grip, in close-ups of her face her body is facing the other wall of the room, perpendicular to the floor. In shots showing her and her hands on the lever, her body and head are facing the floor. (00:35:55)
Continuity mistake: When the two Cybermen meet the Dalek for the first time, they are exterminated. They fall directly in front of the Dalek, but when the camera angle changes to show the second Cyberman hitting the floor side on, you can see the Dalek in the background. The Cybermen both fell straight forward, so it shouldn't have been possible to see the Dalek when seeing the Cyberman side on in the next shot, as the Dalek is facing them both directly.
Continuity mistake: When Martha is walking up to the hospital just before the motorcycle gear-clad slab bumps into her, her right hand goes from by her side to holding her purse strap between shots. (00:02:15)
Continuity mistake: When Martha is talking to the Doctor, who is posing as a patient, about her encounter with him in the street earlier, which he doesn't remember, she takes her stethoscope off her neck. The camera cuts to the Doctor, then back to her, and she's taking it off again. (00:04:15)
Continuity mistake: Martha reaches her right hand up to open the window, prompting Julia to panic and say "Don't! We'll lose all the air!" When the shot changes as Martha points out that the windows aren't exactly airtight, her right hand is suddenly lowered. (00:09:47)
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)
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 telling Martha that he was just wandering and not looking for trouble, in the wide shot, he's rubbing his chin. In the close-up immediately afterward, his hand has jumped to his hair. (00:19:45)
Continuity mistake: When Martha and the Doctor are talking in the alley at the end, he's leaning on the TARDIS. His exact position keeps changing between shots. (00:39:10)
Continuity mistake: When the Doctor puts his tie back on after returning from the morning, the collar of his shirt is noticeably askew as a result. Just moments later, when Martha enters the TARDIS for the first time, the collar is neat again, without him having done anything. (00:41:00)
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)
Continuity mistake: When Lilith has Shakespeare under her spell and is having him write an alternate ending to his play, there is one shot of his face where his quill can be seen in the corner, perfectly still, even though the next shot shows that he's writing. (00:18:25)
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.