Luke 1:20+34 record responses from two people to surprising angelic news- Zacharias is told that his wife will bear a son, and Mary is told that she will bear a son. The responses are less similar than the news.
Zacharias and Mary both asked for clarification. It would seem that Mary asked from a heart of faith; Zacharias obviously asked from a heart of doubt.
So it's OK to ask God about things we don't understand; it's OK to ask the Bible questions when we don't "get it." But we may never ask these questions from a doubtful heart that does not assume on faith the truth of God's Word.
The failure in our understanding is ours; we are not the judge to whom evidence must be presented, but the child to whom wonders must be explained.