Other mistake: When the Doctor and Donna get onto the roof, after he sonics the door shut behind them, as they run for the crane for the window washing cart he puts his sonic screwdriver in his mouth, holding it between his teeth, and pulls something out of his pocket. It looks like he might be carrying Miss Foster's sonic pen - except that at this point in the episode, it hasn't yet been revealed. (00:24:20)
Other mistake: After Jack uses Davitch's information to complete the Controller's coordinates, the Doctor uses a remote to project a holographic, transparent screen of the location in question. The image shows Orion's Horsehead and Flame Nebulae. In a shot immediately afterwards, looking through the holo-screen back at the Doctor and company as he explains what's going on, the image of the nebulae is not mirror-reversed as it should be, but is the same orientation as in the previous shot. The kicker is that the image of the nebulae has been altered, as well: it's already been mirror-reversed - in the actual sky, the Flame is left of the Horsehead. (00:38:40)
Other mistake: When Mr. Thursday goes to see Vastra, to hire her to investigate his brother's death, he doesn't see her face (she's a Silurian "lizard woman from the dawn of time") until she lifts her veil to take a closer look at a photograph he brought her, upon which he faints. However, Vastra's veil is quite see-through, enough that her non-human appearance is obvious to the audience even before she lifts it. The same thing happens when she goes to visit the coroner later - although he doesn't faint.
The End of Time: Part Two - S4-E18
Other mistake: Shortly after everyone arrives on the Vinvocci ship, when the Vinvocci and the Doctor run through the door on their way to the flight deck, the Doctor comes back to get Wilf, who didn't initially follow because he was mesmerized by the sight of the Earth from orbit. It's obvious that David Tennant went just behind the door and paused briefly before coming back into the room, which is not what the Doctor is supposed to be doing. (00:16:00)
Other mistake: The Doctor says: "He's taking the suspended-animation chamber to the church." The subtitles say "[...] to the judge." (00:15:30)
Other mistake: Clara says "The dark, the sword, the forsaken, the temple." The subtitles say "The Doc [...]." (00:22:10)
Other mistake: The Fisher King says "The Time Lord... Lied." The subtitles say "The Time Lord... Night." (00:35:00)
Other mistake: The line spoken is "You mash up Vikings to make warrior juice." The subtitles say "You must have [...]." (00:12:30)
Other mistake: As the Doctor passes a stack of three cubes, the camera is close enough to see the top cube has two small squares intertwined on the side facing diagonally toward the light. He said all were the same, no difference or individuality whatsoever. (00:03:53)
Other mistake: Near the start, the Doctor and companion, just after having experienced a violent earthquake within the city of ancient Pompeii, discover someone sold the TARDIS after fleeing toward where they parked it and finding it gone. But where it had stood there is a floor to ceiling shelf of clay pots, very aligned, unshaken, unmoved from the shelves. (00:04:00)
Other mistake: Just before the Doctor ignites the atmosphere, Sylvia's house is getting dangerously full of gas. When Sylvia and Wilf go outside after the air is cleared, the inside of their house is completely clear. Meanwhile, back at the Rattigan Academy, there is still gas lingering in the air. (00:34:43 - 00:37:15)
Other mistake: As Amy, River and The Doctor enter "the Underhenge" River says "More than just a fairytale." This is a reference to The Doctor saying pretty much the same thing to River at the end of S5 E5 when she says she will see him again "when The Pandorica Opens." This moment has not happened for River yet, it is still in her future. So how can she "call back" to it? (00:11:48)
Evolution of the Daleks (2) - S3-E5
Other mistake: After the hybrid Dalek Sec explains the Daleks' plan to harness the power of a solar flare to the Doctor, when the Doctor asks how many minutes until the flare arrives, Sec says it's in 11 minutes. A fair amount of action and backstabbing later, when the Doctor and Laszlo arrive at the top floor of the Empire State Building and after the Daleks take back control of the elevator, the Doctor says that the solar flare arrives in 6 minutes. It is a considerable stretch for everything that happens between those two moments to take place in only five minutes.
Rise of the Cybermen (1) - S2-E8
Other mistake: Alternate Jackie is said to be turning 40. According to a newspaper Mickey finds early in the episode, the parallel universe is in the same year as the main universe. When Jackie's age (she claims to be only turning 39) is announced at the party, Rose does not in any way react as though that's different from the age of main-universe Jackie. The problem is that, given that Rose was 19 when she met the Doctor, and it has been, for main Jackie and Mickey, likely at least two years since the events of "Rose" (remember Rose's one-year accidental disappearance), this means Jackie would have had to have gotten married, and had Rose, before she turned twenty, and been a widow by the time she was twenty. Given that Jackie is from the UK, a first-world country, and that she seems to be in her twenties in "Father's Day", this is highly unlikely.
Suggested correction: "Highly unlikely" is not impossible, there are many cases of this sort of thing happening even in the age of contraceptives. The episode is also set during the 80's, so it's possible that Pete and Jackie were misinformed. There are other TV shows such as Raising Hope or Bump that use this as a major plot point - hell, the very next episode after Fathers Day features an approximately 12-year-old mother in the form of Nancy, the 17-year old mother of antagonist Jamie.
The Day of the Doctor - S7-E16
Other mistake: Billie Piper is listed as playing "Rose" in the closing credits. Rose was certainly mentioned, yes, but Piper in this episode was actually sentient superweapon the Moment, who merely took Rose's form, and was in all other respects nothing like the former companion.
Other mistake: When the Earth's nuclear launch sites are being brought online, country by country, in preparation for a strike at the Sontaran ship, Russia is puzzlingly omitted, even though North Korea of all nations is included. (00:17:20)
The Christmas Invasion - S2-E2
Other mistake: When Rose and Mickey are running across the plaza after being dropped off by a cab, a fence is visible between where they are and where the cab pulled up. It is unlikely to say the least that they would have gotten out of their cab right by a fence and climbed over it. (00:08:45)
Utopia (1) - S3-E11
Other mistake: The stet radiation in the red room is able to disintegrate living beings, with the exception of the immortal Jack. People not going in the room are shown to stay out of the line of the door when it's being opened, lest they be disintegrated. When Jack comes out of the room after having finished in there, the Doctor, telephoning the rocket, is in line with the open door yet remains completely fine. (00:35:15)
Utopia (1) - S3-E11
Other mistake: When Professor Yana shows Martha his pocket watch, which she comes to realise is a Chameleon Arch, she initially finds it familiar from the appearance of the back, and eventually asks him if she can see the front. Before she eventually sees the front of the watch, there is a shot where the front is hidden to the camera, but should be perfectly visible to Martha, just as Yana says "It's old. It's not meant to be." (00:34:40)
The Impossible Astronaut - S6-E2
Other mistake: After River shoots at the astronaut going into the lake, she drops her arm. The next second, she turns around and the gun is holstered without her having made any movement to do so, and there was no sound made.
Suggested correction: The holster is low enough for the subtle movement her right arm makes to be using it. As for the sound, the removal of her gun doesn't make a sound either. The only sound heard is directly before it when she put her medical scanner away.