At the start of the two-parter, it was established that the Chula ambulance is mauve because that's the universally recognised warning colour, and that no one but humans uses red. And yet, at the end of this episode, when Jack tries to open it up and triggers an alarm, there's a red light flashing on the panel. The ambulance itself is mauve, the security protocols in the event of the ambulance thinking it's under attack is Red.
The nanogenes must at least understand that humanity is divided into genders. We hope. Otherwise they might have doing more changes to people than the episode lets on.
They seemed to know something wasn't working right, as they fixed everything as soon as Nancy hugged Jamie, giving them a proper template to compare him against. Maybe all the seeming supernatural stuff (connecting to speakers, telephones, typewriters, etc.) were just the nanogenes trying to find someone related to check their work against. Or maybe that's a designed feature to avoid this sort of thing.
Speaking of nanogenes, the ones on Jack's ship are correctly programmed to fix humans, but what about Time Lords? When they heal the Doctor's burned hand, do they transform it into a regular human hand? For that matter, what do they make of his extra heart?
The over the top hamminess of the Doctor's joy at the Everybody Lives moment makes perfect sense once you factor in which Doctor we're dealing with; this is the Ninth Doctor, he's (certainly by his perspective) still fresh out of the Time War, where, as far as he knows he wiped out his as far as he knows own species. Since then in every one of the adventures we've seen thus far, at least one person has died, in several the survivors are outweighed by the dead. For that Doctor? Everybody Lives is a big deal.
