Revealing mistake: When Lilith bespells Shakespeare to write the end of Love's Labour's Won the way the Carrionites want it, there are several shots where a white fleck of some kind is visible in the lower centre of the screen, stuck to the camera lens. (00:17:10)
Revealing mistake: After arriving in New New York's undercity, the Doctor and Martha find a screen playing the news. The Doctor tinkers with it and gets a video of flying cars passing a picturesque view of the city. This is a clip from the last episode set on this planet, "New Earth" - the fact that in a close-up of the screen, the TARDIS can be seen parked on the cliffs as it was in that episode clinches it. (00:03:55)
Evolution of the Daleks (2) - S3-E5
Revealing mistake: When Dalek Sec picks up the remains of the radio and turns it in his hands, the "Hamilton" label on the front of the radio is written backwards, indicating that the shot has been flipped horizontally. (00:05:00)
Evolution of the Daleks (2) - S3-E5
Revealing mistake: When the people in Hooverville are meeting around the campfire, it's raining. However, everyone's clothes and hats are completely dry. (00:28:05 - 00:28:45)
The Lazarus Experiment - S3-E6
Revealing mistake: When the Doctor and Martha get out of the elevator and enter the reception room in search of Lazarus, they pass by the string quartet. The violinist and cellist are only miming the actions of playing, as their bows aren't actually touching the strings of their instruments. (00:18:05)
Revealing mistake: In the close up shot of the boys' machine guns firing, in the background a white truck can be seen driving across the green countryside; not appropriate for the time period of the story. (00:25:25)
The Family of Blood (2) - S3-E9
Revealing mistake: In the penultimate scene, with Tim Latimer helping an injured Hutchinson across a muddy battlefield at night, one of the shots is flipped - in the unflipped shots, Hutchinson has his right arm slung across Tim's shoulders, but in the flipped shot, it appears to be his left arm, and the two young men have switched sides. (00:39:45)
The Family of Blood (2) - S3-E9
Revealing mistake: The pyrotechnic mortars used in the destruction of the Family's ship are visible in the shots leading up to their detonation. As the Family run from their ship through the field, the mortars are visible against the branches behind them. Shortly afterwards, they detonate, creating the illusion that the invisible craft has exploded.
Revealing mistake: When the Doctor goes to toss the trio of Christmas balls up, the two times after the first toss are re-used shots of the first toss. His movements of his right arm to bring up the controller are too exact to be coincidence. (00:50:15)
Revealing mistake: At the end when the Doctor makes it snow, in the wide shot you can see the snow blows in from the left side, showing that they used a snow machine just off-camera. (00:54:30)
Revealing mistake: Max Capricorn is a cyborg, with his head being the only remaining part of his original body, wired up to a mobile life support system. If you look closely during his scenes, whenever he turns his head, the costume the actor is wearing to hide his body becomes apparent, as the wires and cables below Capricorn's head also move slightly.
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.