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: Cthulhu Mythos
Complete Monster: Nyarlathotep differs from most of H.P. Lovecraft's gods. While Lovecraft describes other Outer Gods and Great Old Ones as mindless or unfathomable, Nyarlathotep is a sadist who is fully aware of humanity's existence, and enjoys exercising his power over them. He kills or drives people to madness while disguised as the Haunter in the Dark, drives entire societies to ruin in the form of the Black Man or the Black Pharoah, and generally treats all life as part of some giant cat-and-mouse game.
Hilarious in Hindsight: Lovecraft described Azathoth as a monstrous indescribable thing which resides in the center of the universe, often described as "gnawing" and "chaotic". Scientists now believe that the center of our galaxy (and, by extension, other galaxies), is a supermassive black hole. Perhaps Lovecraft was on to something....
Inferred Holocaust: The bodies most commonly associated with the Yithians? Those belonged to beings native to Earth before the Yithians used their mind-swapping powers to leave their own dying world for ours....
Running the Asylum: An appropriate and positive example - Lovecraft encouraged his fans to use his mythology, and expanded off the concepts within those fics. Indeed, without Lovecraft's fan friends, his work would have drifted into obscurity.
Seinfeld Is Unfunny: Similar to Slender Man in present day, some are considering the character of Cthulhu to be so overused and well-known that he's become a cliché of the Cosmic Horror Story genre. Fortunately, there's plenty of other monsters and villains in the Mythos for writers to use to avert this.
One could consider the interbreeding between humans and the Deep Ones to be this since it's basically people having sex with giant fish.
Too Dumb to Live: The protagonist of "Fane of the Black Pharaoh" by Robert Bloch. Being led down by a cultist, the archeologist sees centuries of prophetic events, notably of visitors being lead down the Fane and soon killed. Guess what happens next?
Unfortunate Implications: Knowing Lovecraft's views on race and religion can cast some of his works into a rather negative light. Other authors tend to avert this.
The Deep Ones are likely a demonization of miscegenation.