POINT 1 - Diligently Study The Context
I suggest to you that these "apparent contradictions" are inevitable, because the Bible is large enough that subjects are considered from different angles.  In cases like this, a study of the context of the statement usually resolves the apparent contradiction.  For example, on the surface, Ephesians 2:8-9 would appear to teach just the opposite of James 2:24.  But when you consider all passages on grace, faith, works, and obedience, and the contexts of Ephesians 2 and James 2, you see that Ephesians 2 is discussing the BASIS for our salvation (how it is earned) while James 2 is discussing whether or not we have to meet CONDITIONS in order to receive the salvation provided for (earned) by the death of Christ. 

POINT 2 - Seeming Contradictions Help Us To Learn Detail
Sometimes these seeming contradictions help us to learn more detail about the subject in question.  In the Ephesians 2 / James 2 example just cited, the "problem" forces us to investigate how the apparently conflicting statements do not contradict.  Knowing that God wrote the Bible, and knowing that God cannot lie (Titus 1:2), we therefore know the Bible can't contradict itself, so we go into an in-depth study of the contexts and other passages to determine how the two passages don't contradict.  Another good example I've heard to illustrate this point is the apparent contradiction between Acts 9:7 and 22:9.  Did the men with Saul hear the voice of Jesus or not?  The answer is that they heard the voice in the sense of hearing the noise of the voice, but they did not hear the voice in the sense of understanding the words.  We commonly use the word "hear" in both those senses today.  This is a trivial example (because it doesn't involve any doctrine), but it does illustrate how an apparent contradiction can help us to learn detail.  If we didn't have both verses, we wouldn't know the detail they the men actually heard the voice, but didn't understand the words. 

POINT 3 - God Wants There To Be Some Work Required
Passages like Mark 4:11-12 and Matthew 13:13-15 teach that God makes learning the truth harder than "falling off log," because he wants a person to love Him enough to show diligence in his study.  II Thess 2:10-12 shows that if a person does not love the truth enough, God will send him a delusion.  Simply put, if a person wants to believe a lie, then God will facilitate that.  John 7:17 teaches that those who really want to know God's will and are willing to do it once they learn it, are the only ones guaranteed to learn the truth.  Half-hearted commitment to Christ (Rev 3:15-16) will never be enough to learn enough of the truth to be set free (from sin) by it (John 8:32).  Spiritual laziness will not cut it with God (Acts 17:11).