Towards the end of the episode, The Doctor states that The Hybrid [of two warrior races] could not have been half-dalek, as "the Daleks would never have allowed that." However, in Doctor Who: Evolution of the Daleks, the Cult of Skaro create such a being out of Dalek Sec, half-human and half-dalek.
When you see The Doctor appear in the teleport machine for the second time, the teleport "special effect" is missing and The Doctor is briefly visible just standing in the chamber waiting for his cue to start coughing. This is not how the effect was seen in the beginning of the episode and subsequent scenes.
At the top of the tower where the Doctor places his skull, as he confesses to The Veil there is a close shot of the Doctor with stars behind him and The Veil's hand hovering to one side of his face, you can clearly see the stars in the dark parts of The Veil's hand, showing that they were superimposed over the scene later.
In the graveyard scene, the Doctor says to the Veil, "Physics of a triangle, you lose!" In the Series 9 DVD, the subtitle for this is given as "Fifty-seventh time, you lose!"
Considering the number of skulls in the water after a just a few thousand years, by the time 2 billion have passed the skulls should be overwhelming the castle.