The short answer to such a protest is context – immediate and Bible-wide. If one faithfully studies out an alleged contradiction, he will eventually be able to resolve the issue. And in the process, he’ll gain invaluable wisdom.
Unfortunately, the “context” defense doesn’t seem to satisfy everyone. In such situations, it might help to use a worldly analogy.
Say, for instance, that someone tells us his dog Bowser bit Joe Blow, and adds that Bowser is one good dog. Sounds contradictory, doesn’t it? But suppose we dig a little and find out that Joe Blow is a veterinarian, and his owner had taken his normally benign pup into the clinic with an extremely painful dental abscess. Or maybe we learn that Joe Blow is a burglar, and Bowser was simply defending his family.
Whatever the explanation, we see that context has resolved an apparent contradiction.
A book I read some time ago shows how this principle can be applied to Scripture – in this case, to show how it’s possible for a believer to be both in the world and of the world.
"If we had only the story of Lot's life as it is told in the book of Genesis, we would never have imagined that Lot was a true believer. But 2 Peter 2 tells us three times that this conflicted, compromised man was 'righteous' -- and more, that he was 'distressed' and tormented by life in Sodom … Ironically, though Lot was revolted by Sodom, Sodom was in his soul. It is possible, then, for a believer to be distressed by the world while willfully clinging to the world." (Set Apart: Calling a Worldly Church to a Godly Life, R. Kent Hughes, 2003, p. 13)
The point is that you could look at multiple biblical references to Lot and wind up being confused: With all that happened with him, how could Peter, writing under the inspiration of the Holy Spirit, call this man "righteous"? But when you look at the whole counsel of God, the answer comes into focus: Lot had not allowed himself to be fully "set apart" for God, which is the very definition of holy. Yet he was a believer, and his God-given righteousness did express itself in his refusal to participate in, or condone, Sodom’s sin.
There are many other biblical principles folded into these thoughts, but I think it’s a good illustration of why a scoffer can’t justify taking a couple verses out of context and saying they contradict each other. Just as we needed more information to determine how biting Bowser could possibly be called “good,” he would do well to look for more information in the face of an apparent biblical contradiction.
Of course, this assumes that our scoffer wants to resolve the alleged contradiction. And that's another issue entirely.