These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
And, more recently, we have thisthing. Apparently, the Doctor's new minions are Body Horror-inflicted humans who have had their sense of self suppressed or overwritten. Aughhh, indeed!
The Scrappy: Shockingly averted so far. It's a diverse cast of characters, but all of them are so interesting and fun at times that there don't seem to be any characters overwhelmingly hated by the fanbase. Even LouisLark still has as many fans as he has haters. The same goes for the Doctor.
Viewer Gender Confusion: A mild example, but Reilly was subject to this during the first couple of chapters. A few people thought that she was a boy for a while - presumably because of her short hair, mostly flat chest, and her name (which can be used for both males and females.) Thanks to a combination of Art Evolution and Word Of God though, this is no longer an issue.
The Woobie: Mr. Porter. He was just a good, kind-hearted, psychiatrist who wanted to help his friend Sonia's family. And then he was brainwashed by his patient. This decent individual was forced to watch helplessly as his new persona, Mr. Friday, killed people for the sake of the Doctor's plans. He was unable to stop it for years and was even forced to watch helplessly as his brainwashed self killed Sonia, the woman he loved. He then met Reilly who unintentionally helped him snap out of it, but she found that she still hated him for all that he had done - justifiably so, from her perspective. It is still very easy to feel sorry for Jack on this page in particular. Reilly looks absolutely horrified at what he had to go through.