Long before New Who for me.
Warriors of the Deep was ground zero for the show proselytizing the kind of crank pacifist politics that Sarah Jane rightly mocked back in Robot.
But it recurred heavily in some of the NA's (Blood Heat) and even some of the Big Finish audios. The point where it really sat ill with me was infact in the climax of the audio story Davros, in which the Doctor declined a clear headshot on Davros in order to claim the moral high ground, even though Davros was holding a woman hostage at the time.
Ironically for the first two seasons of New Who, I dared hope the show had successfully reformed itself from that pacifist insanity, until Sound of Drums came along and proved me wrong.
Though Aliens of London/World War III still sat a bit ill with me for its naked contempt for anyone in the military.
Also I thought The Christmas Invasion was incredibly crass in its digs against Bush, and seemed to show no awareness of the fact that maybe a war-hungry president *is* what's needed during an alien invasion. But of course that wasn't the point, because RTD always has to take us out of the fiction to soap-box at us.
And The Idiot's Lantern had some rather uncomfortable, cheap moments of feminist lecturing and father-shaming. I remember someone saying the reason it sits so ill, despite Mr Connelly being a bully, is that it's interfering with the common culture of the time (and punishing him for being almost no different to any other father of his background), and also it's Rose delighting in being mean to him for meanness' sake, and with no thought to how they might be inflaming an already volatile domestic situation.
I remember feeling unpleasant about it at the time, even though I actually kind of considered myself a male feminist back then (before I became a bit more red-pilled)
So maybe it was The Idiot's Lantern.