For me, it's in the fact that Chibnall has all season chosen "safe" villains - by which I mean, his villains are generally types that PC culture is happy to see as villains. White men, rich corporate Trump-types, that sort of thing. There were a couple of episodes that strayed from this, but overall as a season it felt like Chibnall played it safe, even to the point of cowardly, in his storytelling. And if he'd done it well, I wouldn't personally care. But they were also bland and one-dimensional, and that's harder to overlook. It's seemed at times that he was more concerned with having appropriate villains than with having original stories.
In the long run I feel like it just ended up being unfortunate for JW, who deserved better stories than she got.
And I wonder how much of the feeling about the PC-ness (?) of Thirteen's first season has to do with when folks first discovered Doctor Who. I didn't know the show until its reboot, and Nine and Ten remain my favorite Doctors. During the past several years, I've seen numerous episodes with the earlier Doctors, but I wasn't alive during those years to learn to love them first. And the first four seasons of Nu-Who aren't (IMO) terribly preachy - they're more sci-fi drama/adventure/touch of comedy. Are most of the comments about the past season being more PC coming from people who prefer the RTD and/or Moffett eras, or is it more evenly distributed with those who were fans of the show from its inception in '63?