I hate silly or anachronistic NPCs. E.g., Black Flags over Freeport has an NPC named Billy Bones, who is basically a psychotic Old West gunfighter. Makes me nuts. How are players supposed to take a villain seriously if the villain is nothing but a caricature?
I dislike the use of demi-human NPCs (in human-dominated lands) when a human or half-human NPCs can fill the role just as well. It helps if there're at least a couple of lines on why the NPC is in human lands, but it still bugs me. In my world, seeing an Elf in a human city is a relatively rare occurrence ... it's not just a matter of deciding the local baker is Elven.