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.
Utopia (1) - S3-E11
Continuity mistake: When the Doctor gets the rocket to work by tinkering with the boost reversal circuit, he picks it up with his left hand, sonics it, and then transfers it to his right hand, all in a shot where he has his back to the camera. In the next shot, facing him, he's holding it in his left hand as he pulls something off the device. The shot after that, facing Professor Yana again, the circuit is back in his right hand. (00:18:50)
Utopia (1) - S3-E11
Character mistake: When the Futurekind spy starts sabotaging the silo's systems, and Chantho notes that they're losing power, she says, "We're losing power-tho!" - forgetting the "Chan-" prefix that she starts anything she says with, in order to not swear by her species' standards. (00:27:00)
Daleks in Manhattan (1) - S3-E4
Continuity mistake: When Diagoras enters the Daleks' lab, he is shown pulling on his right glove twice. (00:18:55)
Daleks in Manhattan (1) - S3-E4
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?
Audio problem: When the Doctor and Martha are watching Shakespeare in the Globe, Martha says "He's a bit different to his portraits". After she says this on the left of the screen the Doctor's head comes into shot and you can clearly see by his facial expressions he is saying something to Martha, yet no sound is heard. (00:06:10)
Evolution of the Daleks (2) - S3-E5
Revealing mistake: When Dalek Sec picks up the remains of the radio and turns it in his hands, the "Hamilton" label on the front of the radio is written backwards, indicating that the shot has been flipped horizontally. (00:05:00)
Last of the Time Lords (3) - S3-E13
Continuity mistake: Just after the Master destroys the gun in four parts, there is a shot from exactly the same angle and the bag it was in has disappeared. There is then a shot from the other direction and the wreckage is still there. (00:28:35)
The Sound of Drums (2) - S3-E12
Factual error: When they are running over the bridge, supposedly in London, you can see the Heddlu sign on the police station (Heddlu is Welsh for police). You can also see a Cardiff bus at the bus stop underneath.
The Sound of Drums (2) - S3-E12
Continuity mistake: When gassing the cabinet members, the Master puts on a gas mask. The Valiant logo is above the tube, and upside down. In the next shot, it is below the tube, and the right way up. (00:04:50)
Evolution of the Daleks (2) - S3-E5
Revealing mistake: When the people in Hooverville are meeting around the campfire, it's raining. However, everyone's clothes and hats are completely dry. (00:28:05 - 00:28:45)
Factual error: The establishing shot of Bedlam Hospital shows it with 18th-century neoclassical architecture, in an episode set in 1599, in the Elizabethan era. (00:23:20)
Continuity mistake: When Sally Sparrow is about to take the key from the weeping angel, at first the key is on a piece of string, and that string is wrapped around the weeping angel's left hand. In the next shot, and when she pulls the key out, the string is now only in the angel's palm. (00:10:30 - 00:11:10)
Evolution of the Daleks (2) - S3-E5
Continuity mistake: When Martha is searching for how the Daleks changed the design of the Empire State Building, she is examining the plans for the top of the tower. In the first shot where the new plans are visible, the upper right shows a more detailed picture of a plate of Dalekanium. Seconds later, when we can see the new plans again, it's the same side view but the enlarged picture of the plate with the Dalek bumps is gone. These are still the same new plans (the old plans are on her right) and there was no time or reason for Martha to take another page. (00:24:40)
Continuity mistake: The meteors are shown approaching and hitting the ship on the starboard (right) side. Twice, however, they are erroneously described as being to port (left): When the meteors are first seen on the scanner by Frame, and later when Frame tells the survivors in Kitchen 5 to go starboard because the port side of the ship is impassable.
Other mistake: When Sally is taking the key from the angels, she squats down out of the frame to reveal an angel behind her that has lowered its hands from its face. When the shot cuts back to Sally, there is another angel standing in front of the window on the other side of the room whose hands are also lowered from its face. The two angels with lowered hands are directly across from each other: they should have been frozen in place from this point due to their quantum lock.
The Sound of Drums (2) - S3-E12
Continuity mistake: In the conference room, Saxon (The Master) puts on a gas mask that has an emblem mounted above the hose. After replying to the question, he moves the mask, and the emblem is on the bottom of the mask.
The Lazarus Experiment - S3-E6
Continuity mistake: When the Doctor is saying goodbye to Martha, he's leaning on the open TARDIS door with his hand open. When Martha says that things just kind of escalated, the Doctor's hand is suddenly a fist. (00:02:00)
Daleks in Manhattan (1) - S3-E4
Continuity mistake: When Frank is dragged off by the pig-slaves, the manhole opening into the theatre is depicted as completely open from below. When the shot switches above to the stockroom when Solomon pushes the Doctor away from the manhole, the lid is resting half over it, before it being completely open when Solomon moves to pull the lid over the manhole and close it. (00:23:14)
Daleks in Manhattan (1) - S3-E4
Continuity mistake: When the Doctor turns the newspaper towards Martha so she can read the headline, in the wide shot, the corner in his right hand is bent back towards him. In the close-up showing the headline, the corner is straightened with his hand in a different position. (00:04:29)
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 for all of his crimes hurts him more deeply than death would.
Captain Defenestrator