This is particularly true with longer books (raising hand--like mine!) and when the copy editor's idea of how to write a book differs from the writer's own personal style.
Don't get me wrong: writers are not perfect (at least I'm not) and every copy editor so far, including the worst, has caught a mistake I'm glad he/she caught. There's a reason to have someone look over a manuscript word by word, punctuation mark by punctuation mark, and question the dubious choices a writer made, or fix the obvious typos, extra spaces, missing quotation marks, etc.
But then--as all writers with more than one or three books out knows--there are the other copy editors. Personally, I make excuses for them as much as I can because it's not an easy job at the best of times, and when you've got a fiction book (harder than anything but highly technical non-fiction), a book in a genre where made-up words and names and places are common, and a writer with marked stylistic bent, you're dealing with a book that's going to require more than the ability to spot that incomplete sentence and teh where the should be. I accept that it's really hard to figure out whether the writer erred or is making a creative decision that works for that book and that writer's audience.
However, on hot muggy days with the fan on in the kitchen, going through 658 pages of text full of marks the writer does not agree with, the writer may begin to feel that the excuses have been stretched past their elastic limit. The more days it takes (because every single mark must be considered both individually and in context: does it make the book better--neutral--worse?) the closer to breaking that stretched excuse comes.
Some copy editors, from the get-go, show that they have an ear for fictional prose and dialogue, as well as respect for the writer's individual style and ability. Others...not so much. In my experience, those who leap to "fix" what isn't wrong also often miss what is...so the writer must be alert, on this close reading to unintended echoes and infelicitous phrasing that the copy editor hasn't marked. Those who put little question marks and maybe an "awk?" or "echo" in the margin are preferred over those who scrawl their own words to replace what they don't like.
I suspect that copy editors who don't seem to have much "ear," and who apply the rules of grammar and punctuation suitable for a college essay to a novel, don't read much fiction themselves. Especially not quality fiction. A friend of mine discovered, by asking, that the copy editor working on a recent manuscript had not read any of the previous books and also had never read English (as opposed to American) fiction. Yet what works in an essay on the judicial system in medieval France (for instance) will not work in a novel.
Fiction has another purpose than explication: it creates an alternate reality into which readers (if lucky) fall for the duration of the book. When I read Keri Hulme's The Bone People I am not here: I am in New Zealand, among people unlike those I met there--and yet so real I feel I would know Joe and Kerewin and the rest if I saw them in a pub. When I read Perez-Reverte's The Sun Over Breda, I am not here: I am in 17th c. Flanders, with a Spanish tercio, hungry, cold, ragged, held to duty by a very different sense of honor. Those writers--all fiction writers--accomplish the goal of immersing the reader in the story using every element of the language--including those not found in grammar texts.
This, again, is why copy editing fiction well is so difficult. If writer leaves out "that" as a relative pronoun, trusting readers to fill the gap--"He knew they were coming" instead of "He knew that they were coming"-- or if the writer puts it in, the change in pace conveys something. A writer may choose an older spelling (still recognizable) to suggest a difference from everyday life without going into Elizabethan English pronoun and verb forms. Fiction used to be read aloud more than it is now, but even now many readers "hear" the words as much as see them. (Audio books are restoring the place of sound to fiction--a good thing, if they're well-voiced.) So the best copy editors for fiction hear what they're looking at and recognize that every word and every punctuation mark has its place in creating that immersive experience. Only the writer knows for sure what that experience was meant to be.
Writers are supposed to have the right to "stet" any change they don't want, though for most of us a blanket stet would be a stupid choice. But given that the book sold to a publisher in the first place, and has been through the editorial sieve already, it behooves copy editors to take it on faith that the writer isn't stupid and has a reason for his/her decisions. (My worst-ever not only thought I was stupid and ignorant, she basically said so on the manuscript in a couple of snarky notes in the margin. This was several books back: not the present situation.)
At any rate, even the mildest level of red marks on a page is likely to make a writer uncomfortable. Cover the page with them, and the writer will begin to mutter and complain to his/her family and friends. And checking them will take longer than the writer hoped.
On the other hand, if the writer catches the mistake the copy editor didn't, and finds some new tweaks to make, then the writer gets a tiny burst of glee.