Frontier in Space. Not the story overall, but a specific bit in it where the Doctor and Jo are imprisoned by the Master, and whilst under camera surveillance the Doctor manages to sneak out whilst Jo bluffs that she's still having a conversation with him. During which she tells the Doctor she needs to be a bit kinder to the Master. Now sure in one sense it's probably a bluff with an air of flattery because the Master's watching, but it also feels like an improvised patronizing attitude filtering into the show itself, possibly from Manning if it was unscripted. Of saying 'oh the Master isn't that bad or scary, and the Doctor should play nice and get along with him'. It also feels wrong coming from Jo, when she would've had colleagues in UNIT she'd known and lost because of the Master's activities.
The Time Monster & The King's Demons. I still think it's pretty dumb for the Doctor to plead the Master be spared in either story, given that the universe would be a safer place without him. the King's Demons is probably the worse example because the Doctor should've surely wised up after Logopolis.
Warriors of the Deep (quelle suprese!). A story in which the Doctor decides to protest everything and nothing about war and the military, including the fact that humans understandably try to fight back and defend themselves when war is forced upon them, when seemingly he'd prefer them acting like the pacifist suicide cult he seems to demand here. So what is it's message? That victims of a genocidal militia's ethnic cleansing should feel proud they maintained some moral high ground by dying passively, and those that didn't and fought back got what they deserved?
Whatever it's message the story seems to have no choice but to ensure anyone sane enough to disagree with the Doctor is killed off slavishly taking a bullet for him just to prevent its bullshit being exposed. It ends with the Doctor learning nothing, still seemingly convinced his disastrous suicidal approach would've worked and the humans were all at fault for refusing to listen to 'reason'.
Like I said, this just seems to be the point where Doctor Who became a zombified version of itself continuing a zombified version of its ideology, under makers who clearly don't know what they're doing.
Battlefield. I still find the militant feminist politics of this leave a sour taste in my mouth. Not only is the Brigadier treated like an unforgivable sexist for offering Ace a blanket, but he's seemingly expected to respect Lavelle's female independence enough to leave her wounded and alone in a combat zone whereupon she ends up getting outnumbered and murdered by Morgaine.
Curse of Fenric. A minor bother but I really don't like its seeming critique of Britain's World War II actions whilst saying nothing about what the Soviets did. Particularly the rather indigestible idea of the Soviets having greater faith in the Motherland and revolution than the Christian Brits, given the totalitarian nightmare Stalin's Russia was, especially for the military. It was a fear-driven, not faith-driven culture.
The Idiot's Lantern. The Doctor and Rose's lecturing and belittling of Mr. Connelly for being generally no worse than any other family patriarch of the time. Made worse by the fact they completely abuse his hospitality to do it, and succeed in only bear-baiting him. Oh guess who'll bear the brunt of that later when he decides to furiously reassert his manhood?
Daleks in Manhattan/Evolution of the Daleks. Only really the last confrontation scene with Dalek Caan. The scene wants to make out that the Doctor's power of mercy and forgiveness (which just seems stupidity at this point) is enough to subdue a Dalek that could kill him any moment, and worse, is enough to scare it into running away. Way to undermine the Daleks completely, Fathead.
The Sound of Drums/Last of the Time Lords/End of Time. It seems Logopolis has been completely forgotten now, as the Doctor seems to be ridiculous about his ability to offer the Master untold levels of unconditional forgiveness, because he's the only other survivor of his world. This never made sense to me. To my mind if I was the Doctor and had lost all those loved ones, it would utterly make my blood boil that the Master of all people survived and yet the rest of them didn't.
What's frustrating is they could've easily explained it that the Doctor needs the Master alive because the human futurekind need Professor Yana restored to human form to help them survive. But no, because RTD always goes the overwrought emotional route, and would rather downplay the sci-fi arc element incase it scares the soap viewers away.
Let's Kill Hitler. Kind of connected to the above, but the last thing you should include in Doctor Who is a scene of the Doctor stressing that he never would've saved Hitler's life unless it was strictly an accident, particularly when Last of the Time Lords, Journey's End and End of Time are in recent memory where the Doctor did extend a saving hand to what are arguably meant to be worse mass-murderers than Hitler was.
Into the Dalek. There's something really smarmy and nasty about the way Clara needles the Doctor for his inflexible prejudice against Daleks (at least in Rose's case she saw the Dalek being a victim of torture, and saw that it was evolving human mercies, but Clara just seems to be acting like a vulture eager to criticize the Doctor on anything she can spot). But it gets worse when she smacks him because apparently she knows what he's thinking about feeling vindicated about there being no 'good' Dalek. And it makes no sense given that Clara herself has been a Dalek and knows how they think, and witnessed them nearly murder Gallifreyan children. But the story wants to push a message of the Doctor needing to overcome his prejudices and listen to women, so Clara decides to teach him with the back of her hand.
The Ghost Monument. That stupid scene where they're under fire from robots, and Ryan wants to shoot back but Jodie's Doctor won't let him because guns are bad. Yeah it's more important to endanger them all by stubbornly soap-boxing during a life or death situation, than that Ryan dare shoots a single robot that's not even alive.
Arachnids in the UK. How can I care about the threat of the spiders if the Doctor insists they're not an urgent enough threat to need shooting? Plus the final scene seems to have to give the Queen Spider a death scream, even though it's something spiders have never done, just to show how bad it is that Robertson shot it and ended its misery. That one sound effect has to bear the pressure of justifying a moral point being made by writers who clearly don't know what they're doing anymore.