Other mistake: When Amy's age is given as 1306, the computer screen reads 1308 instead. (00:15:50)
Other mistake: When the Doctor tells the Atraxi "Oh, you're not the first lot to have come here, there have been so many," one of the monsters shown from their scan of Earth is a group of Ood. Even if in one of their uprisings they attacked the Earth, it would have been in the far future. The Doctor has had no encounters with them on Earth, and he knows them to be peaceful, so why would they be amongst the aliens who have threatened the planet? The only Ood who has been to Earth at this point is Ood Sigma, and he didn't come to attack. In addition, a group of Hath is also shown. These aliens have never been seen on Earth at all. (00:53:30)
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)
The Time of Angels (1) - S5-E4
Other mistake: At the end when the Doctor is seen shooting the gravity globe, he does not actually move his finger but the pistol still fires.
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.