Continuity mistake: The Doctor is in a room talking to Amy, Rory and everyone else. He sits at a table where there is a house of cards. The house of cards changes between shots. (00:21:56)
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 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: When the Doctor is watching Jimmy and Adam at the end, his hands go from clasped in front of him to tucked in his pockets between the wide shot and the close-up. (00:40:37)
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)
A Good Man Goes to War - S6-E8
Continuity mistake: Rory threatens Madame Kovarian with a sword. It's on her neck, then in the next shot the sword is not touching her. (00:23:38)
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)
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.
Revealing mistake: When River grabs a gun off one of the soldiers she just knocked out with regeneration energy, the actor sits up slightly, even though the soldier is supposed to be unconscious. (00:24:44)
Continuity mistake: When the Doctor is talking to the Voice Interface Amelia, when he starts saying that "Scotland's never conquered anywhere, you know, not even a Shetland", his left arm, which was stretched out along the railing in the previous shot, is suddenly lowered. (00:27:28)
Continuity mistake: When the Doctor is talking to the Amelia voice interface, in a shot of him from behind his position slumped against the railing is different from shots of him from the front. (00:27:37)
Revealing mistake: Mels is shot in the stomach by Hitler, leading to her regeneration. Rory, when checking the wound, says he's going to try and stop the bleeding. However, when she stands up while glowing with regeneration energy, and in every scene afterwards where Mels/River is wearing that dress, there is no bullet hole or bloodstain visible.
Other mistake: When the Doctor gets George's psychic cry for help, he's shown reading the message without opening the wallet containing the psychic paper. This despite the fact that all previous instances of the Doctor receiving psychic messages this way has required him to open the wallet, suggesting that the wallet itself does not display the message. (00:02:02)
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)
Continuity mistake: When Purcell is sinking into his carpet, just after a shot where he's shown having sunk into the floor up to his waist, we see a shot focusing on his dog where Purcell's legs are visible as he falls forward onto his hands, despite his legs having already been pulled under. (00:23:38)
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)
Revealing mistake: When the landlord, Purcell, wakes up on his floor because his pet dog is licking his hand, we see a few pieces of dog food fall from his fingers - should have been a re-shoot, but all credit to the actor, he knows it has happened and is quick to hide them again. (00:38:38)
Continuity mistake: When Rory brings the unconscious Amy inside the TARDIS and puts her on the floor, the Doctor drapes his jacket over her twice. (00:39:44)
Continuity mistake: As Lucy goes down the hall, she opens door 214, then 215. As she comes to the next door on the right, she opens 214 again, rather than it being 216. This is particularly noticeable because the third room she enters is "her" room, containing her greatest fear - and the first room she went into numbered 214 had a completely different fear. (00:00:56)
Continuity mistake: When the Doctor tells Howie that he should continue telling himself the situation is a "CIA thing", he puts his arm around his shoulders twice. (00:11:22)
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.