Yes

For more information see Doctor Who (1963-now)

Too many to list.

(but most from Moffat and Chibnall😂🤣😂)

Moffat had unfinished plots? Hmm?

@Najawin I feel like Moffat did not have plot holes as much as unanswered questions or things that were not delved that the audience would have easily enjoyed seeing explained. There are a few of both…

• Lorna and the Gamma forests from A Good Man Goes to War is the first that comes to mind. I think we all assumed there was going to be an episode where the Doctor traveled there looking for River and found a young Lorna, but instead we just assume that happened off screen.

• What happened to the Kovarian chapter? We get a one line explanation in The Time of the Doctor of why Madame Kovarian and the Silence were pulling strings in series 5 & 6, but we literally never see them again and don’t know what happened to them.

• Why didn’t the Silence just kill the Doctor it would have been so easy… they blow up the TARDIS but don’t do it while the Doctor is in there, then get River to kill the Doctor but don’t notice it’s actually a robot, but the Doctor can’t remember the Silence when he can’t see them so it would have been really easy to just follow him into an alley and zap him to death.

• Did Brian ever wonder what happened to Amy and Rory? I know they had that short animated sequence about their son going to see him but seeing as that should have been filmed and not ignored I’m including it as a problem.

• When did River fall in love or get close with Doctor? The skip from Let’s Kill Hitler and The Wedding of River Song gives no explanation for when River and the Doctor got close from her perspective, and every time we see River after this it’s late in her timeline.

• Why did Missy want Clara to be with Doctor? Nobody knows because it was never explained…

I’m sure there’s a lot more if you rewatch it and notice these things.

@Dreamleak

The first was answered in an annual published at the same time

The second was filled out with a fifth Doctor audio (and their plans had already been stoped by that point) (this however is a fair criticism)

The third same reason the Daleks and cyberman don’t just kill them.

Four a Minisode release on a DVD

Five several minisodes on the red button and dvds

Six Missy is just like that. (Fair criticism)

@Anastasia Cousins fair point about The Silence… I suppose that was nitpicky.

Everything else I knew about or had seen except for the published annual, I’ll have to look that up. While I understand there being answers to these plot problems, for all of them you have to go outside the main show, and some of that list felt important enough to be in the main show.

@Dreamleak Because Missy thought that Clara being a Control Freak paired up with the Doctor, a man who should never be controlled, would create the most glorious chaos.

It was all said in "Death in Heaven" and "Hell Bent".

@TimeLord11 I don’t really remember Clara being a control freak or Missy saying that

@Dreamleak There's a line in Deep Breath about Clara being a control freak, but I have to say outside of that I don't really remember it being much of a part of her character. Most writers ignored it and I don't remember Moffat doing much with it either.

It's pretty inarguably a part of her character imo.