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.
Plot hole: Martha tells the kidnapping couple to switch off all their engines so the Macra don't notice them. Yet during this scene, the car remains hovering above ground, meaning the engines must be engaged in some way, and the Macra should still hear them. And these things don't hover when deactivated - the car was shown to be parked on the ground at the start of the episode.
Plot hole: The guy working for the Daleks offers the homeless men in Hooverville a dollar a day to go into the sewer because the Daleks need more people. Most of the people refused and one called it slave wages. If they were not getting paid until they came back, and since the Daleks were planning on experimenting on them, the people weren't going to come back; why not offer them a large amount of money big enough to entice them but small enough not to be suspicious?