Continuity mistake: During Donna and the Doctor's conversation with an Ood at the reception who she approaches to ask if he's all right with being a servant, in shots facing the Ood, he's holding his translator ball higher than he is in wide shots and shots facing Donna. (00:11:50)
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.
Character mistake: After the Carrionites kill Lynley, the Master of the Revels, by using the doll to make him drown on dry land, the Doctor says, while examining the body, that he's never seen a death like it. In the Third Doctor serial "The Mind of Evil", involving a monster that could make people relive their worst fears, a character died in exactly that fashion. (00:13:10)
Continuity mistake: After Ida retracts the roof to show the black hole, there is a shot where the Doctor and Rose are looking at it, with nothing above them, as he explains about it. However, other shots of the base's control room show that there are things in the room, such as wires connecting the central computer table to the walls, that should have been visible. (00:08:00)
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.
Character mistake: When the Doctor and Rose are walking back to the TARDIS at the end, he explains to her that Queen Victoria was hemophiliac. She wasn't. She was a carrier of the disease due to a mutation in one of her parents' reproductive cells (probably her father, Edward, Duke of Kent, because he was in his fifties when Victoria was born), but since she only had it in one of her X chromosomes, she didn't actually suffer from it as the gene for it is recessive, which is why most hemophiliacs are male. It is true that several of her children inherited the gene, and one of her sons was hemophiliac, but not Victoria herself. (00:40:55)
Factual error: By halfway through the episode, the plot is alternating between following Clara and Jac in London, the Doctor in the fictional Central Asian country of "Turmezistan", and Kate in New Mexico. Despite the three locations being scattered all around the world, only in London is it depicted to be nighttime at any point in the episode. Central Asia and the southwestern USA are both shown to be daytime, despite the two locations being over halfway around the world from each other, and the events all taking place at roughly the same time.
Revealing mistake: Mels is shot in the stomach by Hitler, leading to her regeneration. Rory, when checking the wound, says he's going to try and stop the bleeding. However, when she stands up while glowing with regeneration energy, and in every scene afterwards where Mels/River is wearing that dress, there is no bullet hole or bloodstain visible.
Plot hole: When the Doctor realises that something is coming up from below ground, he tells Nasreen and Tony that at the speed the three transports are coming, the underground arrivals will reach the surface in 12 minutes. The rushed preparations that ensue, including hurrying from the drill hall to the old church and setting up a surveillance network outside, couldn't have taken less than 12 minutes to set up, especially given that they also had to: inform the others trapped inside the shield (Rory, Ambrose and Elliot), inform Rory and Ambrose that their significant others (Amy and Mo) were missing, run between the old church and the block of houses and gather supplies. And, lest we forget, there's also Rory and the Doctor arguing about what happened to Amy and Ambrose's initial skepticism as to what is occurring.
Plot hole: At the beginning, when the Doctor, Clara, Angie and Artie get off the TARDIS, the two kids are absolutely convinced that they're on the Moon, despite the Doctor explaining that they're actually at the Spacey Zoomer ride on Hedgewick's World, the greatest amusement park in the universe. The kids only realise they really aren't on the Moon when Webley emerges from inside of a fake rock formation, followed by the soldiers. The part of the room that the soldiers come from, which should have been fully visible to the time travellers from the beginning - in fact, they should have been looking directly at it when they leaned out of the TARDIS in the very first shot - looks nothing like the Moon and contains a sign for the Spacey Zoomer ride and a large map of the amusement park.
Factual error: The Vinvocci ship is said to be orbiting 100,000 miles above Earth, later refined to 105,000 miles. That's one-third of the distance to the Moon, and the Earth's apparent size from the windows of the ship is far too large for them to be that distance, or even 100,000 kilometres above the Earth's surface. Judging by the Earth's apparent size, the spaceship is actually orbiting 6,000-7,000 kilometres above the planet's surface.
Plot hole: After getting out of the Pyrovile escape pod, the Doctor and Donna start running back to Pompeii. In the process, they are somehow able to outrun what appears to be a pyroclastic flow. Pyroclastic flows can reach speeds of up to 700 kph, and should be impossible for them to outrun. (00:38:15)