The biggest problem associated with questioning the Bible is the tenancy to assume the Bible is wrong unless proven otherwise. Furthermore, that proof is usually based on how well it agrees with a secular perspective. This is definitely not a legitimate way to question the Bible because you are not really giving it a chance. There is a legitimate approach of questioning the Bible but it requires giving the Bible a chance to actually be correct.
Most of the time when someone supposedly takes a skeptical look at the Bible it is more of a cynical look at the Bible. In other words, most people you talk about questioning the Bible are just looking for excuses to reject it completely. This is an approach where the Bible is assumed to be in error unless it is proven otherwise by agreement with secular sources. This by its very nature would tend to go against the Bible, by not really give it a chance. This is one reason why this is a tactic that is commonly used by someone who is actually seeking to dismiss the Bible rather than looking for the truth.
The main reason why the Bible is likely to disagree with the secular perspective on a topic is that the secular perspective is often atheistic in nature. For example, the secular theories that are presented in the guise of science that tend to conflict with the Bible also assume absolute naturalism, while the Bible is a highly supernatural description of history. For example, the Biblical account of the exodus of the children of Israel from Egypt contains a lot of supernatural events, including the plagues that God brought against Egypt. Furthermore, both the Creation and the Flood are direct supernatural acts of God. They both had natural consequences, however if they occurred has described in the Bible and you tried dating the age of the Earth or even some historical events based on the presupposition of absolute naturalism you would inevitably get an age that is much older than it actually is. Consequently, the Bible will inevitably disagree with a theory of history that assumes absolute naturalism.
Legitimately questioning the Bible requires looking at the world from a theistic perspective. Furthermore, both science and history need to be allowed to take Biblical descriptions into account. Every occasion where the Bible seems to disagree with either science or history, either the Bible is being misinterpreted, the theory being dealt with is being misunderstood, the theory being dealt with makes unbiblical assumptions, or some mistake was made that produces the unbiblical result. One example of such a mistake, is the history of Egypt, where certain starting assumptions have artificially stretched it out, placing the evidence for Biblical events earlier than they should be.
You can legitimately question the Bible, but you need to do it from a perspective where the Bible can be right even if it disagrees with secular sources on the subject matter. Simply put you need to look at the evidence from a Biblical perspective and not an atheistic naturalistic perspective. If you question the Bible in such a manner inevitably the Bible shows that the Bible is indeed true.
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