If your program is about time travel, there are bound to be plot holes, so it stands to reason that Doctor Who is riddled with them. Many of these plot holes aren't even time related, however, and merely point to overlooked details or dropped stories. From Davros's reality bomb that had to go off in some parallel universe to supposedly fixed points in time constantly changing, rules are often broken on the show, leaving gaping plot voids the serpent in the Thames could easily pass through.
Adventures with a Time Lord may not make sense to us humans, companion or not, so we can always use that as an excuse to ignore some of the worst Doctor Who plot holes.
The Doctor Is Part Human
Fans of the 1996 Doctor Who TV movie, which starred Paul McGann as The Doctor, might recall a tiny detail that was dropped like a meta-crisis Doctor on Bad Wolf Bay: the Doctor is part human!
The tidbit of information, which dealt with the Doctor having human ancestry on his mother's side, was totally dropped, never mentioned again in the series. If it were explored further, it would mean changes to everything from his part-human copy, left to grow old with Rose Tyler, to his similarities with River Song. If he's not a complete Time Lord, after all, then shouldn't he have more limitations?
River Song's Imprisonment
It makes absolutely no sense for the Doctor's wife to be locked up for a crime she didn't commit when she's got similar abilities and resources at her disposal. It's meant to be endearing and fun, how she breaks out all of the time to get up to her own shenanigans, but why should she be locked up in the first place?
Song is the only being who makes Daleks quiver with fear, moaning, "Mercy!" while she points a gun. Why would she stick around a jail cell even for this facade? And given the adventures we know she's had since, exactly how long does she even stay in that cell in the first place?
Reapers Should Be Everywhere
What happens when a time paradox occurs on Doctor Who? Reapers come out of the woodwork and attack, of course. Rose Tyler learns this lesson the hard way on "Father's Day," and we're meant to use this information to infer why creating time paradoxes is a bad idea.
Except there are tons of time paradoxes created throughout the show and the reapers just don't show up. Were they like Christopher Eccleston, a one-time thing meant to excite us into jumping into the series again? Given how many times we've run into so many other species it really makes no sense that they aren't more prominent in the show.
What Happened To Gallifrey?
"The Day of the Doctor" explained a lot of things, including what happened to the Doctor's home planet, Gallifrey. Frozen in time after being tucked away in a pocket universe, the planet was open for the Doctor's travels in the ninth series. But how was this accomplished?
Two entire seasons of the show were spent on trying to free Gallifrey, yet suddenly it was free without any explanation. It would seem as if writers might want to put in something about how this happened after spending so much time on the issue, not to mention give fans the satisfaction of seeing it unfold.
People Are A-OK After Life-Threatening Danger
Time after time, regular people on the show survive incredible odds with little to no consequences. A prime example is during "The Power of Three," when people who've suffered cardiac arrest are totally fine hours after their hearts have stopped.
It's great that The Doctor, Amy, and Rory are able to reverse the shock that sent these people to their demise, but it's completely ridiculous that the victims would still be alive after all this time. Even if they survived, they should still suffer some pretty harsh consequences, such as brain damage. It's much more realistic when people meet their ends after episodes like these.
Orson Pink Shouldn't Exist
Meeting your boyfriend's descendant is pretty much standard procedure in a Doctor Who episode, so the fact that Clara meets one of Danny's descendants from the future shouldn't raise any eyebrows. The fact that Danny perished before he was ever able to have kids, of course, is where the problem lies.
How could Orson, or any of his ancestors, even exist if Danny was gone after "Dark Water?" Did he have secret children he didn't know about? Was his DNA saved somehow in order to manufacture clones or be used by a futuristic fertility clinic? This makes no sense any way you look at it.
Matt Smith Shouldn't Have Been Able To Regenerate
"The Impossible Astronaut" is a fantastic episode, but it's full of plot holes. Per the War Doctor, the Eleventh Doctor is on his last life, so he shouldn't be able to regenerate as he does following the first shot meant to incite the regeneration before the second one takes his life. Admittedly it goes down a bit differently, but he also uses regeneration energy to heal River's wrist.
Neither of these ought to have been possible since "The Day of the Doctor" was added into the timeline, but who could have predicted that kind of incredible drama? The War Doctor might be the favorite of many a fan but he certainly left some gaping plot holes.
The Stranded Ponds
After all he's done and all they'd been through together, one would think that the Doctor would have stopped at nothing to return Amy and Rory back to their time. Even if he couldn't take the TARDIS to Manhattan at that time, surely he could have landed nearby in a time close to theirs and traveled to them in another way?
River Song's Vortex Manipulator might have come in handy in this episode, among other things, but instead the Ponds were written off as a plot device, leaving fans wondering why the heck the Doctor didn't do anything about it.
The Statue Of Liberty Was A Weeping Angel
Nope. There's no way this could have ever been a thing. It might be a creative idea, but it also makes no sense. "The Angels Take Manhattan" left us with all kinds of feels, confusion and disbelief among them.
If the Statue of Liberty was a weeping angel, why didn't it go around attacking people? And assuming it did, then why wasn't its movements ever noticed by the thousands of people looking at it all of the time? A missing 305-foot statue seems like something people would freak out about. And given that someone would always be watching it, how could it even move in the first place?
Are Daleks Related To Tribbles?
Tribbles, rabbits... Daleks must be able to repopulate at the same caliber of some of these animals because despite the fact that they were supposedly wiped out, they keep coming back--in droves. Sure, it was one at first, but then it was more, until finally they were flying all over England like homicidal Mary Poppins.
Either they were "exterminated" or not, and obviously they weren't. Perhaps the Doctor shouldn't harbor such guilt when he obviously didn't complete the job he thought he did. It's also dubious how the Doctor doesn't know so many of them exist after all of his travels.