Her sideways look, and grin, at the camera as she said: "Run, you clever boy. And remember", is what makes me think there's something we're not being told.
And another thing! How convenient that the whole nano-conversion thing was forgotten about when Rory realised the Doctor had given Amy his bracelet.
Yes, that look at the camera disturbed me, but I wasn't aware that she was the actress who was going to be the companion later, so I didn't make any connection there. That makes sense. As someone said earlier, I do hope they use her name Oswin instead of Clara -- it's much better. Maybe that was a bit of misdirection?
I wonder just what parts of Amy got converted before it was stopped? That seems likely to become relevant later.