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.
YMMV: The Pilgrim's Progress
Anvilicious: Very much so, and actually the reason it became popular: it was so anviliciously religious that the Puritans considered it as suitable for reading on Sundays as the Bible itself.
Designated Evil: One of the characters Christian comes across is Ignorance; a pleasant, friendly young man who tries to get into the Celestial City by doing good works and living his life according to Jesus' example, rather than simply through faith. He gets thrown into Hell for his arrogance.
Misaimed Fandom: Of a more Insult Backfire type of way. Muckraker in the book is a character who is so obsessed with cleaning up mud on the ground that he fails to notice a golden crown above him. Journalists in the early 20th century who investigated big corporations were dubbed "muckrakers" as an insult, but it eventually turned into a positive term thanks to Theodore Roosevelt's speech "The Man With the Muck-Rake", which notes the irony of the nickname.
Values Dissonance: Uh, yeah, some. "Abandon your wife and children" isn't generally considered acceptable even as an allegory these days. Also, Ignorance's fate can come off as unnecessarily harsh and arbitrary. ("Look, sorry, you really need to go back and follow the proper path. You've done nothing wrong, so we'll hold a spot for you.")