Continuity mistake: When Ambrose, while standing with Elliott, admits to killing Alaya, in the first shot, Elliott is standing in front and to the right of Ambrose. In the second shot, he's standing to her left. (00:27:52)
Continuity mistake: In the last scene, when Amy attempts to seduce the Doctor, she pulls his suspenders off his shoulders and he pulls them back on. As a result, the suspenders change position between shots.
Continuity mistake: In the scene at the beginning with the boy on the Vator being sent "below", the Smiler in the lift is shown with its head turned to its frowning face shortly before it is shown changing its expression. (00:02:23)
Continuity mistake: When the Doctor first meets Liz 10, during their conversation, her hood is pulled completely over her hair in shots facing her, but some of her hair is sticking past her hood in shots facing the Doctor.
Factual error: When the TARDIS is flying over London at the beginning, the London Eye is visible. It's supposed to be 1996, and the Eye was built later than that, for the new millennium celebrations. (00:00:30)
Continuity mistake: During the scene on the hospital roof, when the Doctor is telling off the Atraxi while simultaneously choosing a tie out of several he stole from the locker room, the number of ties draped around his shoulders and the position of his hands changes between shots. (00:52:35)
Continuity mistake: At the end of the hospital roof scene, as the Atraxi are flying away, the Doctor is seen reacting to the TARDIS key in his jacket pocket heating up twice. (00:54:20)
Visible crew/equipment: When Amy is guesstimating Amelia's age, the camera pans to the right and into a crew member's arm. (00:13:49)
Revealing mistake: As Amy stands where she is told, a cable comes towards her feet. As it does, a black thread can be seen pulling it up to wrap around her leg. (00:21:39)
Continuity mistake: As Amy first enters the TARDIS, the Doctor comes up from her left, says his line, and leaves from her left. When the angle changes, he passes in front of her from her right.
The Time of Angels (1) - S5-E4
Continuity mistake: When the Doctor and Amy are in the museum looking at the Home Box, after they steal it, they run to and enter the TARDIS, which is parked at the end of the hall by the last glass case. However, in the first shots of them in the museum, the camera was pointed directly at that spot, and the TARDIS wasn't there. (00:01:30 - 00:02:00)
Audio problem: After landing, the Doctor comes out and jumps in place several times. As he does, the sounds of his landings don't sync up with his motions. (00:04:55)
Revealing mistake: When the TARDIS dematerialises and causes wind to blow against Churchill and Amy, their clothes are affected - but the cigar smoke in the air is unaffected, and actually drifts towards the vanishing TARDIS. (00:14:25)
Continuity mistake: Throughout this episode, Amy's earrings seem to disappear and reappear.
Amy's Choice - S5-E7
Continuity mistake: When Rory and Amy are running from the Eknodine, there is no mud on Rory's back, but he was thrown on his back into mud a minute before. (00:23:06)
Continuity mistake: Generally, it seems like it's cloudy on a rooftop, or Atraxi ship is making a shadow on it, but for one moment, after Doctor comes through the hologram, we can see bright sun and a shadow of construction behind the camera.
Factual error: The all important date of 26/06/2010 and it ticks over on Amy's alarm clock right at the end of the episode. However it shows 11.59 AM and flicks over to midday (12.00PM) the next day. The date should've stayed on 25/6 or, as I suspect was the intention, the clock should've read 11.59 PM and then ticked over to 12.00 AM thus changing the date correctly. (00:41:00)
Other mistake: As Amy, River and The Doctor enter "the Underhenge" River says "More than just a fairytale." This is a reference to The Doctor saying pretty much the same thing to River at the end of S5 E5 when she says she will see him again "when The Pandorica Opens." This moment has not happened for River yet, it is still in her future. So how can she "call back" to it? (00:11:48)
Plot hole: When the Doctor realises that something is coming up from below ground, he tells Nasreen and Tony that at the speed the three transports are coming, the underground arrivals will reach the surface in 12 minutes. The rushed preparations that ensue, including hurrying from the drill hall to the old church and setting up a surveillance network outside, couldn't have taken less than 12 minutes to set up, especially given that they also had to: inform the others trapped inside the shield (Rory, Ambrose and Elliot), inform Rory and Ambrose that their significant others (Amy and Mo) were missing, run between the old church and the block of houses and gather supplies. And, lest we forget, there's also Rory and the Doctor arguing about what happened to Amy and Ambrose's initial skepticism as to what is occurring.
Continuity mistake: As the Doctor stares down at young Amy, he takes a perfectly red apple from her and bites it. When the angle changes, and he spits the bite out, the apple has changed to an ordinary red and green one. (00:06:05)
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.