Probably my largest author headache has been defective books. I've been lucky in that I've only had two -- Paradise Island, the galleys of which were published minus the ending of the novel, and Blade Dancer, the hardcover edition of which has a page repeat problem.*** And not having a whole book can really ruin the experience for a reader.
It's not my responsibility to deal with the publisher's screw ups, but it's my name on the book. I care, they don't. That's why I've (quietly) been using my author copies to replace defective editions of Blade Dancer since the problem was brought to my attention.
I've now just about run out of author copies of Blade Dancer, so I'll have to think of something else.
***Edited to clarify: This is not a problem with every copy of the hardcover; most editions of Blade Dancer are just fine. Judging by reader reports, about 5-10% of the first print run books are the defective editions.