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.
Big Lipped Alligator Moment: At one point, Jack and Maturin are separated from their ship in a lifeboat, and are picked up by a catamaran full of lesbian Polynesians who have apparently recently castrated their husbands and nailed their testicles to the front of their boat. They are let loose without much incident, with no plot consequences, and it's not even played for fanservice. Its main purpose seems to be a giant setup for the image of a female Maturin with a flaming sword 'castrating left and right'.
Fridge Logic: In The Ionian Mission, Stephen acquaints Diana with the basics of Andrew Wray's scrublike behavior, including the fact that he cheated Jack at cards, and Diana herself is aware of Wray's nature. How, then, did she so easily believe Wray when he told her that Stephen had been brazenly cheating on her? One would have supposed that, knowing what she did, she'd have been quite wary of anything he told her about Stephen and Jack.
If her lines in The Letter of Marque are any indication, Wray never told her directly. He was content to intercept letters and let the rumors—particularly those concerning Laura Fielding—do their work.
Hilarious in Hindsight: At one point Jack asks Stephen to check up on his current crew's religious affiliation after one sect's beliefs threaten to cause trouble. Stephen's report includes the fact that Jack's cook "worships the Devil" (he's a Yazidi, a Caucasian sect who believe Satan repented). This became a Hilarious in Hindsight because of a controversy over the Royal Navy employing a Satanist in the late 2000s.
On another occasion, (described in one of the earlier books written in the 1970's), Stephen leaves some important secret papers behind in a hired carriage, which causes him much distress and embarrasment (though the papers are later retrieved). In 1990, during the run-up to Desert Storm, a British officer left a portable computer containing important classified documents on Coalition plans in a car he had been test-driving; the computer was soon recovered in that case as well.
Squick: Not all that many examples in the series, considering the often-gruesome nature of the wounds Maturin has to treat; however, in Master and Commander, there's an incident in which Maturin is having dinner with a fellow doctor who has just been dissecting an ape. Maturin looks for a sharp knife to cut his beef, and finally finds it under the body of a young woman that the other medico has been autopsying. When his dinner companion wonders if the knife should be washed, Stephen casually replies that all it needs is a wipe.
It was a dolphin, the catlin was under her flipper.
Actually, it was a young woman. Stephen looked under the dolphin's flipper first but couldn't find the catling there, then lifted the sheet, checked around the woman's cadaver and found the knife he was looking for.
In fact, most of the relatively few examples of Squick in the series have to do with Stephen's casual attitudes toward the corpses or parts of corpses he acquires for study. This produces an amusing moment in one of the later books where Stephen sets aside the body of one of his patients for later dissection just before a sea battle, and it gets buried at sea along with the regular KIA's, much to his dismay. His ghoulish tendencies are a large part of the reason he and his wife Diana keep separate houses: she has a much less understanding attitude towards a pancreas in the sock drawer.
The way he disposes of two enemy intelligence agents who have caused him and Jack considerable troubles: he shoots them and then dissects the bodies with his natural philosopher friend in order to dispose of the evidence.
All the more devastating because it's reported in such a bald and matter-of-fact manner: Barret Bonden, Jack's coxswain and also a close friend of Stephen's, who has been with the duo ever since the first book, is killed in action in The Hundred Days.
Also in the same book: Diana, Stephen's wife, his partner in a complex and tumultuous romance spanning most of the series, is killed offstage in a carriage accident. We are mostly left to imagine the devastation Stephen must feel.
As we've seen throughout the series, very young boys (as young as eight, in some cases, and probably even younger in at least one case) serve as midshipmen aboard Royal Navy vessels, and are subject to the same dangers and hazards as their adult shipmates. Their maimings and deaths cause considerable anguish to Jack (also providing examples of his being A Father to His Men).
Values Dissonance (or, more accurately, Deliberate Values Dissonance): Although it's considered to be a bad thing, Aubrey is never especially perturbed that his sailors are often arrested for rape once they get back on shore.
Aubrey, being British, is not too fond of the American Revolution, either.
Aubrey is a Tory (in today's terms, a Conservative). Whigs (today's Liberalsnote Well, sort of. Whigs were the first describers and advocates for the sort of laissez faire free-market captialism beloved of modern conservatives. Tories, on the other hand, believed that traditional relationships between workers and landowners were more important than the market, which is why Aubrey refused to enclose the common land in his manor.) were generally sympathetic toward the American cause. Most Americans today don't know that the American Revolutionary War was pretty much as politically divisive in the Britain of the 1770's as the Vietnam War was for the U.S. in the 1960's.
On one occasion after the War of 1812 ends, when the Surprise has just concluded a friendly exchange with an American frigate, Aubrey scoffs at the Americans as "little better than democrats" (in that era, "democracy" was considered to be a grossly inferior form of government by many educated people trained in Aristotelian views) before going on to make complimentary remarks about the particular American frigatemen.
Also note that Aubrey, despite his low opinion of the American system of government, thinks the War of 1812 to be a terrible tragedy and gross mistake even though he does his duty. (It's noted that his opinion is shared by many other Royal Navy officers.)
In Desolation Island, set just before the War of 1812, Jack is commanding the H.M.S. Leopard, the same ship that notoriously fired on the U.S.S. Chesapeake in 1807 to force it to hand over British nationals who were serving in its crew (and almost started a war at that point); Jack freely acknowledges, if mainly in his thoughts, that the British were in the wrong in that incident and that he would have been infuriated at the insult to his country and service had he been American. His command of the Leopard sets up a Chekhov's Gun incident in the next book, The Fortune of War, where he falls under suspicion by the Americans for that reason, being at one point falsely accused of having fired on an American merchantman in peacetime.
Aubrey also turns a blind eye to a seaman's particular sexual practices in the first book, despite the Article of War which mandates the death penalty (for * cough* sodomy * cough* )- but he does ensure that the goat the man practiced upon gets a clean and painless end.
Throughout the series, Jack generally tends to take a live-and-let-live approach toward homosexuals in the Royal Navy; for instance, his main concern about a gay captain in his squadron in The Commodore is not his sexual orientation, but the bad effect on discipline and order that results from the captain's showing undue favoritism toward his partners.
Throughout most of the series, Aubrey takes what has to be characterized as an indifferent view to slavery (though, to be precise, he is following the opinion of his hero Nelson). This view changes DRASTICALLY in The Commodore when he captures a slave ship and comes face-to-face with the horrors of the Middle Passage. This produces yet another Crowning Moment Of Awesome when he has some of the slavers arrested, has them forcibly issued with mops, and thunders at them to clean up the filth on the lower decks.
By contrast with Jack, Stephen is a fervent abolitionist. He never quarrels with Jack about that subject, but in a Noodle Incident he verbally savages a slaveholder in the West Indies (Jack is still surprised that Stephen wasn't called out).
Stephen, in The Wine-Dark Sea, is reported to be a subscriber to a project to resettle freed slaves in Sierra Leone. While many modern observers today view such schemes with suspicion as being at least potentially racist in motivation, those projects were extremely popular among anti-slavery activists in the first half of the 19th century (Abraham Lincoln, for example, supported the American Colonization Society's efforts to resettle emancipated slaves in Liberia).
This being the early 19th century, before Catholic emancipation, Stephen regularly encounters casual anti-Catholic prejudice among the Anglican Englishmen he encounters, including even Jack (though this is unintentional on Jack's part, he sometimes blunders verbally, much to his dismay and embarrassment). Stephen has developed a thick skin over the years for this kind of talk, so he almost always waves it off, sometimes making a quip in reply. (This is, of course, providing that it's essentially unintentional and that his interlocutor apologizes quickly; Stephen will take offense if it's deliberate.)
Jack gets a little better about this after he meets his illegitimate son, Sam Panda, who is Catholic and becomes a priest.
Jack, along with most of his fellow Englishmen, are prone to making unthinkingly bigoted remarks about just about anyone not English. It's important to note, though, that Jack acts far less bigoted than he talks.
The Surprise is explicitly described on numerous occasions as carrying a multiracial, polyglot crew, and it's Jack's invariable practice to treat everyone of a given rank equally.
Jack never treats his illegitimate son, Sam Panda, borne by an African woman with whom he had an affair early on in his career, with anything other than deep affection and respect. When he and Sam first meet, he frets over the possibility that Sophie might get angry, but in fact she proves to be broader-minded than that and accepts him readily, particularly as the liaison that produced him took place many years before Jack and Sophie ever met.
The sailors on the various ships that Jack and Stephen sail on are prone to slaughtering the birds and animals of the remote places they visit by their thousands and tens of thousands, for food or just for sheer bloody-minded fun. Stephen himself is a keen hunter, for foodgathering or for obtaining scientific specimens, but he's closer to modern sensibilities in that he sharply objects to the wanton slaughter of animals, especially if it doesn't have any rational purpose such as obtaining food.
Stephen is a very open-minded and tolerant individual. However, being half-Catalan, he cannot abide a Moor (though he never actually has to deal with one).
One particular personality conflict between Jack and Stephen really sets them apart: Jack is all about honorable fighting, with the biggest ruse he's willing to do being sailing under false colors (which almost every ship did when at war). Stephen, on the other hand, is very much a practical fighter, willing to sabotage his opponent at every stage, and calls out the ridiculousness of being willing to sail under false colors but not to read an opponent's letters.
Though they eventually come to see eye-to-eye through character development. During the hundred days they have a long conversation on the matter after Stephen arranges for dockworkers in the balkans to burn french ships at drydock, and Jack concedes that it is better to destroy the ships this way, as there is far less loss of life.
The Woobie: Stephen. Where to start? He pursues a woman for years, at one point very nearly fighting a duel with Jack—his closest friend—over her. He actually fights a duel over her in India, killing a man who might in other circumstances have become a close friend. He finally wins the lady, only to have her leave him—temporarily—because she thinks, mistakenly, that he has humiliated her with another woman in Malta. Then his daughter becomes—temporarily, at any rate—autistic. And finally, the woman dies in a carriage accident offstage. Not to mention that he gains and loses a fortune several times, and he almost dies from the sting of a (male) platypus, an animal he has longed to see for as long as he has been a naturalist.