The Wedding of River Song - S6-E14
Continuity mistake: When the Doctor compares Amy's inaccurate drawing of Rory to the real deal and laughs, in a shot facing Rory the Doctor is shown lowering the picture, than in the next shot facing the Doctor he still has the picture raised. In addition, his grip on the paper changes from holding the bottom of the page to the side, and it also switches hands. (00:23:33)
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)
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)
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 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)
The Curse of the Black Spot - S6-E4
Continuity mistake: The pirate that Toby cuts on the hand with a sword in order to make him stay in the magazine is gone when the Doctor and Captain Avery return, but reappears on the spaceship at the end with the rest of the crew.
Continuity mistake: As the Doctor talks to Idris/TARDIS, he reaches into his coat. When the angle changes, he reaches in again. (00:18:20)
Continuity mistake: After River shoots the last of the Silence, she turns her gun flat side out, and muzzle up. After the angle change, she does it again. (00:37:58)
Continuity mistake: When the file with the photo of Amy's arm lands in the circle, the thumb in the photo is above the 'T' in 'THIS'. A moment later, the photo's position has turned 180° so that the thumb in the photo is pointed the other way. (00:02:57)
Continuity mistake: When Craig enters the house and falls back when the cybermat is attacking him, his arms are down by his sides, breaking his fall. As he lands, he's suddenly holding the mouse so it can't bite him. (00:25:51)
Continuity mistake: When Amy and Rory are searching the darkened kitchen, the flashlight Rory holds switches hands between cuts when it starts turning on and off. (00:13:52)
The Wedding of River Song - S6-E14
Factual error: During the zoom-out from Earth at the end, the Sun is depicted as far, far too large than it actually appears from Earth. (00:40:03)
Continuity mistake: When the Doctor finds Joe's corpse, he walks up to him and puts his hand on his shoulder. In the next shot, facing Joe, the Doctor is suddenly in a completely different position relative to him, behind him as opposed to next to him. (00:15:06)
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.