1. Recasting the Doctor: Typically I hate the idea of recasting a character in an ongoing series, especially when the new actor looks and acts nothing like the previous one. This is especially confusing when you've never actually seen a regeneration story before and you have no idea what that even is. Even more confusing is watching the first episode with a new Doctor after the regeneration has already happened and trying to figure out why people know the Doctor and yet don't know him at the same time. I always use to think that the characters in the show weren't meant to notice or comment on the new actor but in Doctor Who they do it all the time.
2. Daleks: One of the most confusing things about Doctor Who for someone who has never actually seen the show is that the Doctor's greatest enemy can be easily defeated by running up a flight of stairs. Though they have been able to hover up stairs since the 9th Doctor this was actually accurate in Classic Doctor Who and still confuses me.
3. The Sonic Screwdriver: As the Second Doctor's Sonic Screwdriver is not well known, to most people outside the fandom this is a very misleading name as it's pretty much used for anything EXCEPT actually driving screws. I'm pretty sure that the Second Doctor is the only one who actually used it as a screwdriver.
4. "Dr. Who": The most common mistake made by people who have never seen the show is referring to The Doctor as Dr. Who. Just to add to the confusion in the classic series the actor was actually credited as "Dr. Who" though this stopped around the same time the show first appeared in color. Even more confusing is when you find someone familiar with the Peter Cushing movies where the character's name was actually Dr. Who.
5. River Song: Being that I first started properly watching the series when Matt Smith took on the role I had never seen the Library episodes from David Tenant's run until much later. So when I heard people asking questions like "Who is River Song" my natural reaction was "You've been watching the series longer than I have, shouldn't you know?" or "What are you asking me for? I just started watching this show." I had simply assumed she was a past companion, the fact that had died after meeting the Doctor for the first time and him not actually knowing who she was had totally escaped me.
6. Regeneration: This may sound similar recasting but it's not. This is when you just learn about regeneration for the first time and then find yourself wandering why the Doctor is so afraid of dying when he'd just going to regenerate. Also wandering why he most often regenerates into an old man. This part still confuses me, I mean it's not really extending his life by much when he regenerates into someone who's already near the end of his natural life anyway. It would make more sense to regenerate into someone younger.
7. The Tardis: To someone that doesn't realize it's actually T.A.R.D.I.S. not Tardis, it's a big mystery why they don't just call it a time machine. Of course it doesn't just travel in time, but to the outside observer, that's all it is. It makes sense when you know that it's an acronym for Time And Relative Dimension In Space.
8. New Math: This didn't use to be confusing but since the introduction of the War Doctor and realizing that 10 regenerating without changing his face still counts, I've found that explaining the Doctor's incarnations to someone who has never seen the series before can be quite confusing. I was trying to explain to my ex that the War Doctor is 9, 9 is 10, 10 is 11 and 12, 11 is 13, and 12 is 14 and she just looked at me like I had lost my mind. I'm finding that even fans who understand this are still trying to come to terms with it so it's no wander someone not familiar with the series is totally confused and thinks I need professional help.
9. Old Math: Similarly before I actually started watching the series I honestly had no clue in what order the actors actually went in. And I still manage to mix them up some times. For the longest time because for so many people Tom Baker is their favorite I misunderstood this to mean he was the first because of the Recasting confusion I mentioned before. However now I realize that William Hartnel was the first and Tom Baker is the fourth.
10. Talking your enemies to death: If I had actually put this in any sort of order I probably would of made this number 1. The most confusing thing about Doctor Who for me was that the Doctor never actually fought anyone, he just talks at them and I could never understand why they don't just kill him and get it over with. I mean in every episode of Doctor Who I saw all he ever did was talk while someone was pointing a gun at him and for some reason not using their weapon. Especially the Daleks, they fire their weapons all the time exterminating everything is sight but then the Doctor comes on and for some reason they stop shooting to let him talk. Of course I later discovered that this wasn't always the case and one of the reasons the Master is my favorite villain, especially the Robert Delgado Master is because they actually had legitimate fight scenes not just talking at the bad guy and then the bad guy backs down for some reason. Of course I typically forgive Matt Smith for his speeches for different reasons. One, I'm not a little kid anymore and am actually able to appreciate how good the writing is. Two, the Doctor's at a point in his life where it's much more believable that he can stop an enemy with the mere mention of his name. Three, he's great at acting like he has a battle plan when he's really just making it up as he goes.
So what are your top ten things non-Whovians don't understand about Doctor Who. They can be either from your own experience before you started watching the show or trying to explain things to other people who have never seen it. Or if you have never seen Doctor Who then you can just post about things you don't understand right now.