It seems that Atheists don't do their homework when they read Literature like the Bible. One must engage the Authors of the Bible (Both God and man) and their presuppositions and contexts to understand meaning. It seems that when people don't, they can incorrectly invent any discrepancies in the Bible that they want. The following link is a refutation of an atheist's misinterpretation of Scripture by Douglas Wilson.
A Little Something Called Context