Sometimes, when confronted with an especially un-God-like passage or pair of passages from what we all know to be the Most Amazing Book of all Time, Christians have a rather interesting response along the following lines:
Look, the Bible is the product of dozens of writers working over hundreds of years in the contexts of many different cultures. Furthermore, the actual canon was decided by councils of fallible human beings. Of course it's going to contain errors, contradictions, nonsensical stories, and morally problematic bits!
My first reaction to this is, wait, what was the atheist's original question again? Because whatever it was, it seems to have been answered with agreement.
"How can you say the Bible is God-breathed when it contains X?"
"Because the Bible isn't God-breathed, that's how! At least, X certainly wasn't."
Believe me, I get that the sophisticated mainstream understanding of the Bible holds that such superficial notions as Mosaic authorship and the-real-Luke-writing-Luke have gone out the window. (Actually, that second one never had currency, which only makes me more confused about how Christians ever found the canonical gospels so authoritative.) I get that God influenced the creation of the Bible very subtly. Very, vvveerrry subtly, perhaps by means of butterflies. So subtly, in fact, that…
… that it doesn't distinguish itself from other holy texts on any grounds. And even if some part of the Bible did contain an irrefutable piece of prophecy or other wondrous knowledge, that would at most speak to a need to examine and appreciate the specific writing in question, be it Esther or Jonah or Revelation. And we still wouldn't have much to accept the book as truth apart from the independent evidence anyway.
Consider Darwin's Origin of the Species. It includes a few errors and fallacies, such as (in its early editions) the hypothesis that the landgoing ancestor of whales was bearlike (in fact, it was a carnivorous ungulate, awesomely enough). This suggests that just because Darwin got so much right isn't enough reason to accept any single thing he said; it's the independent evidence that justifies our doing so. Neither Darwin nor the Origin is "evidence for" evolution, merely a recorder and record of evidence.
Religion, conversely, doesn't work like science in that respect; at the end of the day, the texts are the big deal. Any evidence that Paul or Mohammad or Joseph Smith, and/or their texts, were less than divinely inspired (whether their mental or moral faculties are called into question) is evidence against the religion, because the religion doesn't allow itself to go by anything else. There isn't a non-Mormon archaeology of the Lamanites; either you're a Mormon and accept them or you're not and you don't. Religion is by definition faith-based. It's somewhat like how — warning, cliche up ahead — alternative medicine that's demonstrated to be effective is no longer alternative medicine.
Once you concede that your holy book is 100% human and 0% divine, you concede whatever religion builds itself around the book. You can still call yourself a Whateverite, but it's much more a cultural than religious designation, like being a secular Jew. (In my compassion and magnanimity, I allow for exceptions for those areas of religious practice which travel into the realms of philosophy and mental/physical exercise, such as Buddhist meditation, Scientological auditing, or Hindu yoga. Lots of atheists and agnostics practice those — well, maybe not the middle one, but for a few.)
On top of all that, "The Bible" is just an artificial human assemblage that is no more "a book" than my DVD collection is a movie. Which brings me full circle: That phrasing of the situation is just the sort of language that some use to defend its divinity.
It's like a homeopath defending homeopathy by saying "Of course it didn't outperform placebo — it's just water!"
Do I expect ill people doused with homeopathic water to be instantly healed? Do I expect the Bible to read as though every iota and keraia (Matt. 5:18) was dictated by the Lord of All? Nope. I just expect the respective viewpoints to at least distinguish themselves from other pseudosciences/religions. And when they fail to, I'm just not that impressed with "It's because they're all true."