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.
Alternate Character Interpretation: The series-long running gag of Nobby Nobbs's questionable humanity may possibly be explained by him being a half-goblin. Vimes suspects, but doesn't conclude anything.
Captain Obvious Aesop: The ending is jarring for some groups of people. Poles, Jews, Gypsies - all these have been called subhuman, and still are discriminated against, despite having master musicians, heroes and geniuses.
Don't Shoot the Message: This line theoretically supports gay and lesbian rights, but it manages to be very unkind, and the fact that the gel being described is one of the book's villains only worsens the effect:
... Frankly, if a gel wanted to go around with another gel who wore a shirt and tie, trained horses, and had a face like a bulldog licking vinegar off a thistle, then it was entirely her business.
Ho Yay: "Your friend told you to take your trousers off as well..." Also, just what was the deal with Stratford and Flutter's conversation that couldn't be revealed while Constable Upshot was listening?
Moral Event Horizon: Stratford's attempt on the life of Young Sam. Gravid Rust and the Magistrates are revealed to have crossed it three years ago.
Gravid Rust's MEH is so terrible that the book ends with Vetinari implying that he's going to send assassins after himeven though everything has been sorted out. Normally, Vetinari's actions have practically constructive results, whereas here he has already got everything under control and is considering taking revenge anyway, purely out of disgust for Gravid's actions. You know you've gone too far when Vetinari is willing to sabotage (albeit in a minor way,) a nicely wrapped up solution in order to exact justice.
Unfotunately it doesn't come across as very satisfying for the reader to see Gravid get his, mostly because he is The Ghost and thus not really a character which makes it difficult to hate him personally and get much emotional impact from his downfall.