-Scotland insisted on having their own ship. Good for them. But how does it move? Did they actually bother to build engines? If they have that capacity, why not share it with the main UK ship? Or did they prepare to leave Earth earlier, with time to build a proper ship and not just a backpack for a whale? But if the Scottish ship has been long separate and out of communication, then it doesn't make sense that the little girl recognizes Amy's accent.
-Amy was hanging out of the TARDIS. The Doctor hauled her back and clearly had her standing on her own two feet inside. Then he walked away and started yammering, and a moment later she was hanging out of the TARDIS, apparently out of control and clinging to the top of the doorframe. How did she get there? With TEH starting with Eleven inexplicably dangling out of the doors, it seems that Moffat writes a very slippery TARDIS.
-The computer gives Amy's age as 1,306. Did the episode ever give an exact date for what year this is set in? If yes, then we could work out when she was born, thus adding some more data to the timeline questions raised by Rory's 1990 ID.
-Was there a point to the video of the little girl reciting the rhyme about the beast below to the little kid who was being sent down? Or was it just to take advantage of the fact the capacity of nursery rhymes to be really creepy?
-There were plenty of other plot holes and shaky logic here. In a way, it felt almost like an Uncle Rusty episode in that it made really great emotional sense but much less factual sense.
-Did anybody die in this episode? I can't remember anyone dying, though there was mention of past dissidents being fed to the whale. Paging Mister Moffat: it's not that I like seeing people die, but the "everybody lives" thing is special when it's unusual.
-"Right then. This isn't going to be big on dignity." Ha! However, what truly makes this line is that it's spoken as he adjusts his bowtie. Eleven, ILU.