the thing in Rupert Pink's bed bugs me. It doesn't fit in with the resolution that the doctor's obsession with the perfect stealth creatures was just Clara's fault. The thing didn't look like a human (it was blurred but it looked ugly) and it disappeared in a flash of blue light.

Since it's Moffat's episode I'm betting he's planting stuff for later again, like what he did in Flesh and Stone (e.g. the doctor losing his coat mid-scene, etc.)