When you look at the etymology that's clearly a misspelling that has stuck somehow.
Lots of modern English words arose from misspellings (and mishearings) - if one becomes popular, it becomes an English word. That’s how languages evolve, otherwise we’d still be speaking Proto-Indo-European.
Plenty of words are like that. "Apron" was originally "napron" but due to confusion from "a napron" sounding like "an apron" it changed that way.
I personally have always said "kerfluffle", not kerfuffle.
Kerfluffle is a misspelling that has yet to be "standardized", which is why you will only find that misspelling in crowd sourced dictonaries where people have added definitions to justify their misspelling.