What are some of the biggest plot holes in Doctor Who that you still think about today?
Minor ones that irritate you or the biggest plot holes, you’ve never been able to get past. Maybe some that just make you laugh, they’re all valid here.
Any and all mediums!
Edit: This just for fun, not to tear down the show or anything.
Here’s one that I just encountered again because I’ve been rewatching Capaldi’s era:
Orson Pink.
He is supposed to be a descendent of Danny and Clara, but we all know why that couldn’t happen. Is it a plot hole? (Surely not, it’s not like the writer forgot he killed off Danny, that was the same series!) Or some kind of rewriting of history? But how/why? It is annoying.
One of my most recent ones is Ncuti just unfreezing in The Interstellar Song Contest. It’s an awesome moment that I like, it looks amazing and SUSAN 
but the ‘how’ still irritates me a little bit.
I loved The Angels Take Manhattan, loved Amy and Rory’s ending emotionally, and also logically it makes no sense at all that they couldn’t just make a fake gravestone and go meet the Doctor in London somewhere. Or just have River Song pick them up with her vortex manipulator. I had to come up with a whole fanficcy headcanon to satisfy myself about this one.
I wouldn’t call it a plot hole in it of itself, but it’s never made sense in the Three Doctors where 2 and 3 talk about how much wiser and smarter 1 is than them. And defer to 1 on every occasion possible. But shouldn’t 3 be the smartest (apart from flying the TARDIS - since he lost that knowledge as punishment and is still lost at this point) since he has all of 1 and 2s memories/experiences
I get it probably has to do with the respect your elders since 1 looks older but 3 is the oldest as well
I’ve got a few off the top of my head I can think of:
Harriet Jones was meant to lead “Britain’s Golden Age” but the time between Aliens of London and The Christmas Invasion is about nine months. Was Britain’s Golden Age less than nine months? I get that it’s implied the Doctor cut it short by saying the six words but were there no major consequences to him wiping a formative period of history out of existence?
Also, as much I love the Yana reveal, it has always confused me as to why the Master’s human alias is an acronym for the Face of Boe’s last words. Don’t get me wrong, it’s a brilliant moment but it doesn’t really hold up under scrutiny. It is, however, why I still defend the “it was the wrong anagram” reveal; that makes just as much sense as the Master’s name being Yana.
Lucky Day, in the last season, was full of plot holes. Why was a man able to dox an entire government institution’s staff with no repercussions? How did he even do that? Why does a global media scandal immediately disappear overnight because one person gets outed as a liar?
Finally, one thing that has always annoyed me is quite how full of plot holes Heaven Sent is. I love this episode with all my heart but a lot doesn’t add up. If the Time Lords were viewing this in real time and saw the Doctor breaking through the wall, why didn’t they intervene at any point? If the entire castle resets, how did the Doctor leave himself messages? What are the actual mechanics of the Confession Dial anyway? It was at this point in my ramblings that I realised I didn’t care (love you Moffat).
Oh yeah, and WHY THE HELL WAS THE MOON AN EGG? HOW DID A NEWLY BORN CREATURE LAY ANOTHER EGG THREE TIMES ITS SIZE? WHAT ABOUT ALL THE OTHER STORIES SET ON THE MOON, DID THEY NOT HAPPEN? WHAT IS THIS EPISODE?
I’ve wondered this and why the wall itself wouldn’t reset as well
RTD really loves anagrams 
For this reason I headcanon it’s a timey-wimey backronym. The Chameleon Arch Master’s name just so happened to be Yana, no particular significance to it — but, eons later, Jack/the Face of Boe remembered the reveal and was able to use the specific phrasing that he did as a reference to Yana’s name.
(That, or it wasn’t an acronym at all, and the Doctor and Martha simply assumed it was when it was really just a coincidence.)
While I understand what you mean, it somewhat misses the point of their ending. Amy’s entire arc has been deciding between Rory and Doctor Who (See also, Amy’s Choice). As Rory puts it in The Power of Three, they have real life and “Doctor life”, and they will have to choose.
TATM is Amy making that choice. She chooses to have the normal life with Rory, rather than the adventures in time and space, so while they could get out of it, this is the point when they won’t.
Bigeneration being so rare yet it happens twice
The looms don’t work anymore and biology finds a way
Timelord mitosis
I don’t get why this bugs people so much. Time can be rewritten, as they say time and time again. Danny’s death was clearly a change in the timeline, they visited Orson before that change.
It had rather direct consequences. With Harriet Jones deposed, it allowed the Master, as Harold Saxon, to become the next one and do all his evil plan stuff.
My interpretation is that what we see is what slipped through the cracks. We know from Moffat in DWM that the Doctor Who who figured it out left messages everywhere (including one on the back of the portrait of Clara), and when the rooms reset themselves, some messages survived, and became part of the room’s default state.
The way I interpret this is the wall is part of the structure of the confession dial itself, rather than the castle created within it. Therefore, while the dial can repair what it’s created, it doesn’t repair itself. That, or Azbantium takes loads of energy to replenish, and no-one involved in creating the dial ever thought that some idiot would punch it for a billion years or so, so it was programmed not to waste energy repairing the wall
See, this is exactly why I said I do love it on an emotional level, because I agree with you — I’m a huge fan of the character arc and Amy’s ultimate choosing “real life” with Rory.
But on a plot level, the ending leans so hard into “Rory is stranded forever, by choosing to follow him Amy also accepts being stranded forever, there is no way for the Doctor to ever see them again” and does not acknowledge at all that there are obvious ways out that they are either somehow not thinking of or choosing not to take.
I’d accept that if Danny was killed by Missy or a Cyberman or something, or by an accident while travelling with the Doctor.
But he was hit by a car. How exactly was time rewritten? Unless it was Missy behind the wheel 
That’s what I don’t get.
I guess maybe they could have made that a little clearer. Maybe the original timeline where we got Orson was one in which he actually chose to come back instead of bringing back the kid, just in terms of things we saw on screen.
Didn’t Missy plan the whole thing though maybe I need to rewatch the episode
There is a novel short story that says Missy was driving the vehicle in question. (It just said prose on the wiki, guessed wrong)