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) - chronological order
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 Day of the Doctor - S7-E16
Clara: Doctor, what's going on?
Eleventh Doctor: It's a... Uh... Timey wimey... Thing.
The Doctor: "Timey" what? "Timey wimey"?
Tenth Doctor: I... I have no idea where he picks that stuff up.
Trivia: In "Human Nature", when John Smith (The Doctor's human identity) is talking about his parents, he says their names are Sydney and Verity. Sydney Newman was the creator of Doctor Who and Verity Lambert was the first producer. (00:30:00)
Last of the Time Lords (3) - S3-E13
Question: Why does The Master fear The Doctor forgiving him? What's he forgiving The Master for exactly?
Chosen answer: The Master knows that deep down, he deserves death for the crimes that he's committed throughout his life, and since he regards The Doctor as his arch-foe, he expects it to be at his hands. The fact that The Doctor is still willing to forgive him after everything the Master's put him through hurts him more deeply than death would.
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.