They mined too deeply, and too greedily...
I'm amused at the spoiler into Amy's own future, though it does result in the usual questions about time travel and causation. Did future!Amy wave at present!Amy because she saw her past self (with no memory of having done so), or because she remembers seeing her future self do so? Fortuantly the Doctor stops it going any further before bad stuff happens. Curiously we don't see future!Amy and future!Rory again in this episode, so either they were far enough away to begin with, or they remembered and made sure they were far enough away.
Interesting failure of the Tardis' perception filter, though I suppose if someone's actually looking for the police then it'd be hard to hide a big police call box from them. Note for non-Brits: there is a real present-day police call box in London that looks like the Tardis, so it's not entirely crazy for a random passerby to assume that the Tardis is an actual police box (though a random passerby assuming that one parked on a church doorstop in the middle of a Welsh village is a mobile incident room is stretching it).
I do wonder about the strategy of most opponents of the Doctor. The drill has triggered some sort of early warning system, so the reptiles go and capture someone by pulling them through a hole in the ground. Then they capture Amy through the same method, right under the nose of the Doctor. Next they create a localised force field and mount a reasonably successful raid on the few that are left. But then the Doctor traps one in a refrigerated van, and the reptiles... retreat? And disable the force field?
So, the reptiles had the enemy on their knees and then allowed them to go away and get reinforcements? Weird strategy. But fine, both sides have hostages, so maybe they can do a hostage exchange and then all live happily ever after. Except the reptiles have apparently decided to sacrifice their hostage as an excuse to wipe out all the humans. Fine, that makes sense as a gambit... if it wasn't for the previous raid which didn't have the look of someone trying to get taken as a hostage. And for the fact that the Doctor doesn't do that sort of thing.
And if they want to rise up and reclaim the Earth, why have they waited until now to do so? The current crop of baddies all seem to be trying for suicide by Doctor.
Still no arc image, though it is a two-parter. Then again, they've gotten much more complex with their story arcs over the years - back in the days of the ninth Doctor it was just a subtle phrase ("bad wolf"), but now it's more of a concept (cracks in the universe, with the silence coming). I wonder if the reptiles are running from the silence as well?
Hmm, a thought: both River Song and Prisoner Zero mentioned the Pandorica. Could this be Pandora's Box in some form? It almost fits, though classically Pandora's Box is full of generic bad stuff rather than anything spectacularly world-destroying. Then again, modern media has a habit of changing classical mythology to behave however the plot requires: in Tomb Raider: The Cradle of Life the box contained very deadly diseases, while in Professor Layton and Pandora's Box it gave whoever opened it very vivid hallucinations.