The Prioress used to be thought of as the target of fairly light mockery, but in part due to the violently anti-Semitic tale she tells, modern critics have found evidence of a more condemnatory intent. This may well, however, be a case of Values Dissonance.
Terry Jones (yes, thatTerry Jones) wrote a book, Chaucer's Knight: The Portrait of a Medieval Mercenary, arguing that far from being an ideal hero, the Knight was actually an amoral mercenary, and intended as a Take That! against someone Chaucer knew.
Some indication of the factitiousness of Jones's theory may be grasped by his reference to The Teutonic Knights' "Crusade" in Prussia as having attracted a great deal of criticism, thus discrediting the Knight, who had fought there. Though the Teutonic Knights' Polish enemies had denounced the Prussian campaign, it is highly unlikely that Chaucer would have endorsed their opinion, even indirectly, since his own patron (and in-law)'s son had "reysed" in Prussia, and was proud of the accomplishment — even after coming to the throne as King Henry IV. (In comparison, Chaucer does poke fun at the Squire's aspirations towards chivalric gallantry, as he refers to his having fought "in Flaundres, in Artoys and Pycardye," referring to a then-recent military campaign that had been an unmitigated disaster.)
From the opposite ideological angle, while "The Franklin's Tale" comes across to a modern audience as a positive argument for equality and respect in marriage, some have argued that Chaucer intended these features to represent a bad marriage. The franklin is compared to Epicurus in terms of being something of a glutton,note As Epicurus was reputed to be, though there's no real evidence of this. and at the time the philosopher was also known as representing evil atheistic sentiments, but he still wins his argument with the Nun's Priest and the Wife of Bath.
Fanfic Fuel: An Older Than Steam example. The unfinished state of both the poem itself and some of the tales (particularly "The Squire's Tale") has led to poets writing their own continuations, starting almost directly after Chaucer's death.
Glurge: The Prioress's Tale, complete with the unfortunate implications common to glurge in spades. Whether this was intentional is unclear.
Harsher in Hindsight: The Prioress cannot abide cruelty to animals — nor can she abide a lack of cruelty to Jews. Hmmm...
Even back then, there was probably an implication that she had a major case of Moral Myopia (even if the anti-Semitism would be condoned). Some scholars have noted that it was common when writing of virtuous characters to start with good manners and love of animals and then move into their charity toward the poor. Chaucer makes you expect that he'll start talking about her charity, but he doesn't — it's pretty clear she's nicer to animals than people.
Historically anti-Jewish predjudice has often had an Even Evil Has Standards aspect in some corners. It is not implausible to imagine Chaucer disliking Jews while satirizing other anti-Semites, simply on the grounds that "they didn't deserve to be treated that badly."
Nightmare Fuel: Oh, more than a few of the stories have it. "The Pardoner's Tale" is probably the most notable example.
Values Dissonance: Attitudes about a great many things have changed a great deal since Chaucer's time, and some of the tales (e.g., the Prioress's tale, with its egregious anti-Semitism) have massiveUnfortunate Implications by contemporary standards. The trope is inverted by some stories, such as "Wife of Bath's Tale" and "Pardoner's Tale," which would have been edgy or improper in their day, but now better reflect modern values.
Maybe not so much the "The Wife of Bath's Tale," because while the titular character was very independent and had views on women's sexuality that were very ahead of their time, out of her five husbands the one she truly loved was the one who physically and verbally abused her and insulted women in general and actually made her half-deaf. And she still loves him. Furthermore, her prologue shows that she's a little hypocritical: she likes her lifestyle, but she doesn't think all women should do it, and that remaining a virgin is better. She just doesn't want to do it herself. That's all the prologue, though. The tale itself contains a character who is introduced when he rapes a maiden he passes being spared by the queen for her own test instead of being summarily executed, followed by him journeying, getting some help from an old woman that gets his life spared, and though what reads like a moment of indecisiveness, given how he'd been insulting his wife right beforehand, he gets a wife that is young, extremely beautiful, and will always be loving and perfectly loyal to him. Even if he did get that because he let her decide how he wanted her to be, it didn't read like it was because he had actually learned a lesson, even though that was the answer to the question the queen asked him; it read like he disliked both options equally and couldn't decide.
Endless debate rages about whether Chaucer's own point of view would have aligned more with traditional medieval values or with some of his more liberal-minded characters. Cagey SOB that he was, Chaucer intentionally depicts himself an Unreliable Narrator, possibly to provide plausible deniability in case any of his stories attracted unwanted attention.