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.
Parental Incest: The subtext is there. Amy calls her father "my own dear"; "love", etc., sleeps in the same bed with him, takes more care of him than he does of her, is compared to a Greek character who breastfeeds her father in prison, and considers Mrs. General (whom Mr. Dorrit is courting) to be "replacing" her. Squick.
Tear Jerker: John's outburst to Arthur after Arthur lands in the Marshalsea.
"She loves you! The very walls can see it!"
Values Dissonance: Modern readers often have a hard time with the Aesop that concludes Tattycoram's plot, in which she is supposed to reconcile herself to her proper station in life with the Meagles. Likewise, the fact that Miss Wade, an independent woman who has made her own way in the world and who might have been a beneficient and inspiring patron for Tattycoram, turns out to be cruel and completely out of touch with human feelings.
The whole father/daughter vibe Amy and Arthur have going on.