Here's a thing.
Remember these sort of statue guys? The Doctor describes them to Rory thusly:
"History has collapsed. Whole races have been deleted from existence. These are just like after images. Echoes. Fossils in time. The footprints of the Never-Were." (emphasis mine)
This isn't the first time we've heard that phrase. Here's the Tenth Doctor describing the atrocities of the Time War in The End of Time, Part 2:
"The Skaro degradations. The Horde of Travesties. The Nightmare Child. The Could-Have-Been-King with his armies of Meanwhiles and Never-Weres."
Note that the Doctor specifically says that the statue guys are the footprints of the Never-Weres, so presumably real Never-Weres would be somewhat less lame than the Dalek in the museum was. I would imagine an army of things that never existed had been deleted from existence would be pretty freaky, particularly to a time-sensitive species like the Time Lords.
There were some other things I noticed in the episode as well, but I'll post them later after I've had times to get my thoughts relevant screencaps together x.x