The Wedding of River Song - S6-E14
Continuity mistake: When the Doctor and River are wrapping his bowtie around their hands in a handfasting, the length of the cloth changes between the close-up and the wide shot. (00:37:40)
Revealing mistake: When the Cybermat gets free after the Doctor tries to hit it with a pot and accidentally gets Craig instead, it is very obviously CGI when it slides along the floor and stops by a piece of furniture. (00:26:34)
Continuity mistake: When Alex is hugging George after rescuing him from the peg dolls, George's arms are down in shots facing Alex, but his left arm is up in shots facing him. (00:37:23)
The Vampires of Venice - S5-E6
Factual error: Isabella is a black girl living in 1580 Venice. So how is it that she has perfectly straight hair, when modern hair care products won't be invented for centuries?
A Good Man Goes to War - S6-E8
Revealing mistake: Several of the hallways in Demon's Run, particularly the one where Madame Kovarian has the baby brought to her and the one the Doctor's standing in when he realises where Amy and Rory's baby was conceived, are the repainted sets of the TARDIS hallways from "The Doctor's Wife", three episodes before.
A Good Man Goes to War - S6-E8
Audio problem: When Madame Kovarian says, "Give the order, Colonel Runaway," she is seen facing three-quarters away from the camera. Her jaw does not move as she speaks. (00:25:10)
Revealing mistake: Just before Strax leaves grumbling that he's going to play with his grenades, if you look closely you can see his face mask peeling. (00:27:45)
Dark Water - S8-E11
Plot hole: When the Doctor and Missy, the latest incarnation of the Master, meet for the first time, she passes herself off as an android. Only later in the episode, after seeing the Gallifreyan hard drive that she has been uploading human minds to, does the Doctor realise that she is a Time Lady, and he doesn't realise that she's the Master until she tells him in the episode's cliffhanger ending. The problem here is that over the show's long history, Time Lords have been shown to have the ability to recognize each other instantly, an ability that makes perfect sense given their powers of regeneration. Previously in the new series, it was even stated that Time Lords can psychically sense each other, an ability demonstrated on-screen in "The End of Time." In "Dark Water", this does not happen, at all. Now, the Master has a history of using technology to block his/her psychic signal before - the Archangel satellite network from Series 3. However, at no point in this episode or the next one, "Death in Heaven", does either the Doctor or the Master even mention such technology as being used, leaving the mystery of how the Doctor didn't recognize Missy as a Time Lady at the very least a rather glaring hole.
Revealing mistake: During the scene at the beginning where people are taking pictures of themselves with the Cybermen, there are a few moments where the Cybermen's armour is revealed to be rubber when people touch it. (00:02:45)
Continuity mistake: When the TARDIS crashes through the ceiling and lands in the tunnel, the side visible to the camera is not the one with the door. The camera cuts away, and when it returns to the TARDIS, on the same angle as before, the door is now facing the camera, as revealed by the sign and St. John's Ambulance medallion. (00:36:16)
Continuity mistake: In the penultimate scene, just before the Doctor melts Amy's Flesh avatar, he points his sonic screwdriver, snapping it to its full length and opening up the four metal bits around the light at the tip. In the next shot, the screwdriver is "closed", but in the shot after that it's "open" again. (00:43:56)
Continuity mistake: The Flesh, the substance that the gangers are made of, is capable of replicating people and their clothing. However, devices such as the sonic screwdriver are off-limits, which is why there is only one even after the Doctor's ganger is created. This is made clear when the Doctor tosses the screwdriver to his ganger before the ganger Doctor sets off to look for Rory. However, when the Doctor, Amy and the three human factory workers are trapped in the crypt with the overheating acid pool, the Doctor is seen using the screwdriver to scan the acid, even though the device should still be in the possession of the other Doctor. (00:28:57)
Continuity mistake: When Idris/the TARDIS stumbles in the junkyard and the Doctor catches her, just before she tells him that one of her kidneys has failed, her right hand, holding a piece of circuitry, moves between in front of his chest in shots facing him and resting on his shoulder in shots facing her. (00:24:48)
The Christmas Invasion - S2-E2
Continuity mistake: After the Sycorax ship has arrived above London, when Rose has decided that they need to shelter in the TARDIS and is explaining this while preparing to put a housecoat/dressing gown/bathrobe on the unconscious Doctor, the garment jumps between the bed and her hands in a few shots. (00:30:25)
The Unicorn and the Wasp - S4-E7
Continuity mistake: Thoughout the episode, Donna's rhinestone-studded hairband changes between going over or under her ears.
Continuity mistake: The house that Donna and her family are shown living in in Series 4 is different from the house the Doctor dropped her off at at the end of her first appearance, "The Runaway Bride." You would assume they'd merely moved - except that in this episode, Donna and her family are shown living in their Series 4 house before the events of "The Runaway Bride", on the day Donna gets the job that leads to her meeting the Doctor in the first place.
Continuity mistake: In the episode "New Earth", the Doctor said that the titular planet is in the galaxy M87. Upon returning to New Earth in this episode, he says that the planet is 50,000 light-years from where the original Earth used to be. That's a difference of over 50 million light-years, since M87 is a very real galaxy in the centre of the Virgo Cluster, that far away from the Milky Way. (00:02:55)
The Christmas Invasion - S2-E2
Factual error: The episode kicks off with a reuse of the zoom-in from orbit first seen in "Rose." As the sunny North Pole indicates, the Earth is depicted as if it is the height of Northern Hemisphere summer, even though as the title of the episode indicates, it begins on Christmas Eve, three days after the northern Winter Solstice when the Pole is in darkness. (00:00:05)
The Impossible Astronaut - S6-E2
Continuity mistake: When the school bus pulls up to drop Amy and Rory off in Monument Valley, there are no other vehicles in the area. When the bus pulls away, the Doctor has suddenly appeared with a vintage station wagon, parked by the side of the road where it should have been perfectly visible. And he was sitting on the hood, implying he'd been waiting there for a bit. (00:02:45)
The Impossible Astronaut - S6-E2
Continuity mistake: When the Doctor starts walking over to the lakeshore after the astronaut appears, he's still holding the wine bottle in his right hand. In the next shot where we can see his hand, the bottle is gone, without him having stopped to put it down. (00:06:34)
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.