The Impossible Planet (1) - S2-E11
Factual error: The graphics depicting the black hole show matter falling directly towards the centre of it. This would only happen if all the matter happened to be heading in that direction already. In reality, matter approaching the black hole at any other angle would swirl around the event horizon, like water going down a plughole.
Continuity mistake: When the TARDIS arrives back from the formation of the Earth, the Doctor and Donna rush out leaving the TARDIS door open. And yet in the very next shot, the door is closed. (00:44:30)
Revealing mistake: Soon after the Doctor and Donna are blasted back there is fake snow on the camera, indicating there's a camera there. (00:34:15)
Revealing mistake: When the Cyberman arm is shooting at the Doctor and Amy, just after the Doctor jumps out to draw its fire, Amy leans on the Pandorica and you can see it bend in, revealing that it's made out of plastic or something. (00:20:42)
Revealing mistake: When the Doctor and Rose are talking at the bay, the Doctor's hair is blowing in the wind, but it's not when he is shown in the TARDIS. Considering the image of him on the beach is a projection of him in the TARDIS, the two versions should match. The actor was obviously on the beach recording his lines with Rose and back on a set doing the inside scenes.
Continuity mistake: When Mickey enters one of the school's computer rooms, dozens of pupils are busy typing, and every one of them is also wearing headphones. However, once Mickey unplugs the main connection for the computers, and shouts for the students to leave, when the students begin to get up, their headphones have instantly removed themselves from their heads and been placed neatly on the desks next to the computer keyboards. (00:36:25)
The Girl in the Fireplace - S2-E7
Continuity mistake: When the Doctor is trying to fix the connection from the past to the future through the fireplace, the background of the spaceship can be seen behind the flames whilst there is no connection. (00:37:15)
Factual error: Emergency Service vehicles in Cardiff (indeed, throughout Wales) have their signs in bilingual English/Welsh. So the police cars and ambulances seen in this episode should have 'Heddlu'/'Police' and 'Ambwlance'/'Ambulance' bilingual logos. However, the police car seen after the earthquake has its label in Welsh only. (00:40:33)
Revealing mistake: When Mickey closes the wheelie bin lid, he then finds the plastic stuck to his hands, he lifts his hands up and the plastic stretches like tar. If you look closely when he lifts his hands up for the first time, you'll see that a shadow of one of his hands is cast on his shirt, but there is no shadow of the strands of plastic stuck to his fingers. Additionally, when he turns around to pull away from the bin, he crosses the strands over each other, but they are still parallel in the following scene. (00:22:40 - 00:23:10)
The Christmas Invasion - S2-E2
Revealing mistake: After the Christmas tree has cut through the wall in the Tylers' flat, you can see marker pen where the shape has been drawn and cut out. (00:10:30)
Vincent and the Doctor - S5-E10
Factual error: By the time the Doctor and Amy meet him, Vincent van Gogh had already mutilated his ear. He should be missing part of his left earlobe.
Continuity mistake: At the end of the episode, Donna piles suitcases in the Doctor's arms in preparation to leave with him in the TARDIS, and places a striped hat box on top. The bags stay that way for a while as the camera cuts back and forth between them, and you can see the stack of luggage as the camera films the Doctor from behind. Then, as soon as the camera cuts back to the Doctor's face when Donna leaves to give her mother the car keys, suddenly he has one bag under his arm and another in his hand, and the rest of the bags are on the ground with the hat box stacked neatly on top. In addition, when the scene cuts from Donna closing the hatch of her car to her and the Doctor standing by the TARDIS, a large floral-patterned suitcase has appeared, which she was not shown removing from the vehicle. (00:43:15)
The End of Time: Part Two - S4-E18
Deliberate mistake: When the Doctor visits all his recent companions before he regenerates, he goes to a book signing of A Journal of Impossible Things, written by Joan Redfern's great-granddaughter. When she is signing the book for the Doctor, you can hear the scratching effect from the pen but you can see that the pen isn't touching the paper. (00:59:50)
Factual error: The Doctor claims the Daleks are hiding themselves from sonar. But sonar relies on sound waves, which can't travel through the vacuum of space. (00:38:45)
Revealing mistake: At the end when Sarah Jane is walking towards the TARDIS and the Doctor opens the doors, the inside of the TARDIS is obviously a painting. (00:39:00)
The Sound of Drums (2) - S3-E12
Factual error: The army shoot at Martha's car and you can see sparks where the bullets bounce off her windscreen. But, at that close range, one of those things can go through a brick! I know you're supposed to allow a bit of disbelief, but this is taking it too far.
Other mistake: After the Doctor tells Bill that Heather's face isn't symmetrical, when he and Bill look into the "puddle" together the Doctor explains that instead of seeing her normal backwards reflection, she's seeing her face "the right way round." The problem occurs in the next shot of the Doctor and Bill seen in the puddle, because the "WOW!" patch on Bill's jacket is properly where it should be, but note everything else is actually backwards. Things such as Bill's color-block top and her denim jacket buttons are on the opposite way. Also note the Doctor's ring has switched hands. Presumably this shot was edited, and the "WOW!" patch was blurred on the left of Bill's jacket then digitally added to the right side, to give the appearance that it's "the right way round" as the Doctor said. (00:20:15)
Other mistake: When Miss Hartigan is testing the earpod control, the men start off facing her. She instructs them to turn to the right. They turn 90 degrees clockwise. She then tells them to turn to the left. They turn 180 degrees anticlockwise. However, they should have only turned 90 degrees anticlockwise, and end up facing her again. What they actually do is turn on the spot, as opposed to turning left. It takes a further instruction from Miss Hartigan for them to face her again. (00:24:57)
Continuity mistake: When Miss Foster uses her sonic device on the window-washer's crane, she points it at the right-side cable, but it's the left-side cable that breaks. (00:26:25)
Factual error: When Rose gets the message there are two things wrong with what you see on the phones screen: firstly on the top right of the screen you can see the icon for mute even though you heard the beep, and secondly that screen is for when you type in the number you want to call (text), not the screen for receiving a text.
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.