Plot hole: The Atlantic Ocean didn't exist in Early Devonian times (c.400 million years ago), so Scaroth's ship could not have been where the Doctor claimed. The Atlantic was formed when Europe and Africa separated from North America around 160 million years ago and is still growing. What is now the sea-bed was once covered up by several miles of Continental Shelf. The Early Devonian landscape would have been far from barren as plantlife was well established by then. So, either the Doctor's theory that Scaroth's exploding ship caused the creation of life on Earth is wrong, or it was much earlier than he said.
Plot hole: Professor Jones says they tried to borrow the cutting equipment a few weeks ago, but Mr. Stevens says it was yesterday. One of them must be wrong...
The Daemons - S8-E5
Plot hole: It is never explained who - or what - killed the man in the churchyard during the first scene (early in part one). It cannot be Bok (the gargoyle) or Azal (the Daemon) as neither of them have awoken.
Revelation of the Daleks - S22-E6
Plot hole: The DJ fires the ultrasonic gun, to demonstrate it to Peri. The glass in the doors breaks. When The Daleks arrive the glass in the doors is unbroken. It then doesn't break the glass in the doors in any of the other times he fires the weapon.
The Creature from the Pit - S17-E3
Plot hole: The Doctor should not need a book on Tibetan as he already knows the language...he went to Tibet in the Season 11 story "Planet of the Spiders." (Of course, that was Jon Pertwee, the 3rd Doctor. Perhaps losing the mastery of the Tibetan language was a result the regeneration into Tom Baker).
Plot hole: When Jamie and Cully go on the offensive, Jamie lures a quark away from a drilling site into a narrow valley, then Cully drops a boulder onto it. Yet when we see the crushed quark, it is next to a drill, on flat land.
Revenge of the Cybermen - S12-E5
Plot hole: The Vogans live on a planet made of gold. They helped develop the gold weapons that defeated the Cybermen. They know the Cybermen are coming and live in a state of paranoia about that eventuality. So why in the world do they attack the Cybermen with useless projectile weapons instead of "glitter guns" or some other gold-based weapon?
Plot hole: Jo should know what the dematerialisation circuit looks like. She saw it in 'Terror of the Autons', 'The Three Doctors' and several other episodes.
Plot hole: Why is the warning about Sutekh broadcast in English? (It clearly is as the Doctor identifies three E's in the transcript).
Plot hole: One sequence which makes little sense is when Ace triggers the booby-trap gas grenade on the chess board. Although the Doctor places a wastepaper basket over the grenade, the green toxic gas is very much present for the rest of the scene but does not harm either the Doctor or Ace, despite it being shown to have been lethal to the soldiers in a preceding scene. (NOTE: This error only applies the TV broadcast and the original video release; the error was noticed and corrected in 2003 for the DVD release of this Doctor Who story).
The Curse of Peladon: Episode One - S9-E5
Plot hole: The delegate Alpha Centauri is a 'hexapod' - a creature with six legs and feet. ('Hex' = "six", 'pod' = 'foot'.) But throughout this Doctor Who story, Centauri can be seen with all six legs and feet in the air, projecting from the front of the creature... so what is it walking around on?
Plot hole: Leela's decision to stay with Andred is very sudden. They barely speak during the serial.
The Sea Devils: Episode Four - S9-E12
Plot hole: The Doctor and the Master both surface in bright orange diving suits and are the only two wearing them. But when the supposed body of the Master is dragged out it is also wearing an orange diving suit, and the Doctor and Master are still wearing theirs, so a third suit appeared from nowhere.
Plot hole: In episode 1, on both occasions that Silas P presents his card (first to Daphne S, then later to the Doctor), he gives it to his victims the wrong way around. They have to surreptitiously turn it over so that the side with his name on it is facing them, and then act surprised when he tells them to flip the card over to reveal the words "Happiness Patrol Undercover", as if they hadn't seen it before.
Plot hole: Peri makes no mention of the Doctor's heroic sacrifice on her behalf, nor thanks him for it (no wonder he's touchy).
Plot hole: The Doctor and Romana comment on a recording which has finished playing before they have entered the room. Not only that, but all the other characters behave as if the Doctor and Romana had seen this recording.
Plot hole: When Della gets shot in the face in episode four, she clutches her stomach. (What is even more remarkable about this error is that this keeps happening over and over again: someone gets shot and falls to the ground, clutching their stomachs, regardless of where they have actually been shot. See the error in Season 14's 'The Deadly Assassin' for an example of the SAME error occurring).
Attack of the Cybermen - S22-E1
Plot hole: The junkyard at 76 Totters Lane seen in "Attack of the Cybermen" was also in "An Unearthly Child", the very first episode of the show. If you consider London's high land value, it is highly unlikely that an ownerless junkyard would still survive twenty-two years... the local authority would have long since issued a "compulsory purchase order".
Delta and the Bannermen - S24-E3
Plot hole: In episode 3, the swarm of "bees" attacking Gavrok and his men look nothing like real bees, being far too large when they approach the camera's position. (In fact, stock footage of a swarm of locusts was used.).
Answer: It was never destroyed on-screen; it was intact at the end of the TV movie, and destroyed by the start of the 2005 series. It was destroyed in the novel "The Ancestor Cell," but in a completely different manner to what happened in the series.
DaveJB