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 Shadow Over Innsmouth
Accidental Aesop: The villagers do not take kindly to outsiders, to the point that they're worse than the disgusted visitors are. This brings an unintentional "discrimination is a two-way street" message to the story.
"Obed he kinder takes charge an' says things is goin' to be changed ... others'll worship with us at meetin'-time, an' sarten haouses hez got to entertin guests. . ."
Harsher in Hindsight: From the story (Keep in mind this was written 70 years before Gitmo and the War on Terror and, more disturbing, only several years before the Holocaust):
"Keener news-followers, however, wondered at the prodigious number of arrests, the abnormally large force of men used in making them, and the secrecy surrounding the disposal of the prisoners. No trials, or even definite charges were reported; nor were any of the captives seen thereafter in the regular gaols of the nation. There were vague statements about disease and concentration camps, and later about dispersal in various naval and military prisons, but nothing positive ever developed. Innsmouth itself was left almost depopulated, and it is even now only beginning to show signs of a sluggishly revived existence."
Nausea Fuel: They interbred with slimy, ugly fish-frogs from the Stygian depths of the sea!
The air of Innsmouth is usually described as having a pungent stench of rotting fish.
Unfortunate Implications: "The Shadow Over Innsmouth" is generally accepted today as a metaphor for miscegenation: the pollution and degeneration of Small Town Anglo-America by monstrous foreigners. Lovecraft was an extreme racist even by the standards of his own day, which was kind of hard to do considering he was born in 1890. The Deep Ones originally come from Polynesia and the hybrids' appearance - bulging eyes, flat noses, and big, flabby lips - pretty much screams "blackface." The story itself even discusses human interracial marriage in the context of describing Innsmouth:
"But the real thing behind the way folks feel is simply race prejudice - and I don't say I'm blaming those that hold it. I hate those Innsmouth folks myself, and I wouldn't care to go to their town. I s'pose you know - though I can see you're a Westerner by your talk - that a lot of our New England ships used to have to do with queer ports in Africa, Asia, the South Seas, and everywhere else, and what queer kinds of people they sometimes brought back with 'em. You've probably heard about the Salem man that came home with a Chinese wife, and maybe you know there's still a bunch of Fiji Islanders somewhere around Cape Cod."
The blackface-association is more to blame on the later illustrators than Lovecraft who specifically noted that those with the Innsmouth-look do not resemble any normal ethnic group, including Negroid. The fear or racial mixing is there, but not quite that blatant.
The narrator's discovery that his great-great-grandmother was a Deep One, and the fact that this basically dooms him, also recalls the infamous "one-drop rule."