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.
Factual error: When the Doctor spots Rory taking a photo of Prisoner Zero, we're shown a brief close-up of Rory's hospital identity badge. The date of issue is given as "30/11/1990". The main body of the episode is set in 2008, two years before Rory and Amy's wedding in 2010. It's further established in the episode that Rory and Amy played together as children after her first meeting with the Doctor in 1996, with Rory observing that Amy made him dress up as the Raggedy Doctor. Rory could not possibly have worked for the hospital for eighteen years at the time of the episode.
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.