In Luminosity, this is justified and taken to what would otherwise be an insane degree. Allirea's vampire power is making people think of her as unimportant. This is wonderful for The Masquerade, or making people not fight back as she kills them/someone near them.
In the Both Syllables series and its spin-offs, a crossover between Invader Zim and Lilo & Stitch (and Buzz Lightyear of Star Command) explains that Irkens have a low-level psychic power that keeps most people from noticing anything weird about them; Dib and Gaz happen to be immune, though. Jumbaa creates a technological variant to affect everyone in Lilo's town, which is why nobody notices the experiments' oddness unless they already know about them.
While the initial reactions to people Becoming Ponies are not this trope, the reactions in canonically later days are. Octavia's counterpart is completely confused when she walks into a store and gets no reaction other then "Mommy, why is that pony wearing a bow tie?"
Apple Pie from the Pony POV SeriesDark World Arc grew up in Discord's World of Chaos, so naturally things even the rest of the mane six (half of which are thousand year old immortals, one is a wall eyed pegasus, and the last one is a dragon) find a little strange or menacing as daily occurrences. Her reaction to a zombie? About the same a normal person would have to a slightly aggressive dog. She's more interested in the (to her) hilarious paradox that it's both alive and dead at the same time, which causes her to invoke her Logic Bomb power for the first time and convince it it should be dead...which she ALSO doesn't seem to consider strange.
In The Last Human: A Tale of the Pre-Classical Era, humans are so rare that most ponies can't recognize them, mistaking them for some other fantastic anthropoid like a yeti or sasquatch. Thus, when the Human and his companion Star Swirl walk through an Earth pony town, almost nopony bats an eye.
In Seventh Horcrux, Harry Potter has glowing red eyes. This isn't even mentioned in passing until several chapters in, and nobody sees it as a big deal.