Plot hole: The Doctor leaves Martha a recording with instructions for her for when he's human. However, the flashbacks to the incident that led to him using the Chameleon Arch don't leave enough - or any - time for him to have made the recording, presenting his decision to use the device as a spur-of-the-moment one that he immediately acts upon.
Doctor Who (2005)
1 plot hole in Human Nature (1)
Visible crew/equipment: During the warehouse battle, around when the Doctor tells Donna, "Hold on, I'm coming", the film crew can be seen reflected in a door at the right of screen. (00:28:20)
The Doctor: I'm not... I'm not... I'm not from Mars!
More trivia for Doctor Who
Question: 1. Why was Rose not allowed to touch her past self without creating a paradox and causing those creatures to appear and eat everyone, but Amy was allowed to touch her younger self without any repercussions? 2. Why was Rose able to have the time vortex in her head for a few minutes and it only knocked her unconscious whereas the Doctor had it inside him for about 30 seconds and it basically killed him and caused his regeneration?
Chosen answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.
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Suggested correction: He would have been planning the change to human for a while now, not just made it up on the fly. So he could have made a recording before the opening scene.
The episode makes it pretty clear that he and Martha got taken by surprise by the Family's attack. The Doctor also explicitly says, when he gets out the Chameleon Arch headset, that he never thought he'd use it. The flashbacks consistently present his decision to become human as one made as an urgent, in the moment one.