I fear that a list of our pet peeves would become a reference work for those who tend to use them!
A pet peeve of mine is how few people ever reference guides – whether stylistic, lexical, technical … . Ultimately it's the editors' / proofreaders' jobs to employ / follow certain guides for clarity, consistency, and correctness – the three Cs – in their publications, yet now far too many relegate those tasks to computer-automated functions such as autocorrect (which introduces at least as many "typos" as it remedies!) without human oversight.
"Who needs a [style] guide?" is an increasingly common question – and publications that ask it show their amateurism once ink's on paper (or pixels are on screen). I once quit a small, local newspaper because the editor insisted that all writing be published exactly as submitted; that was part of the community's "hippie–anarchist" culture, into which I had considerable difficulty fitting. ;-)
I've compiled numerous corporate / house style guides, from newspapers to academia and beyond, and have often wondered if I were wasting my time. Then I've been brought back from despair's edge when someone has called or written to question or discuss a matter in one of my style guides. Somebody references them, now and then.
"STYLE is knowing who you are, what you want to say, and not giving a damn." — Gore Vidal "STYLE is knowing what sort of play you're in." — Sir John Gielgud "Politicians are not born; they are excreted." ― Marcus Tullius Cicero