Why does the Qur'an agree with the bible in some things and disagree in other things?
The Bible is an important means by which people had access to God's message for thousands of years. It contains many truths from God. Throughout history many prophets were sent by God to guide humankind. The Qur'an teaches that prophets were sent to every people to call them to shun false gods and worship only the one true God. Some of the truths which those prophets taught are recorded in the Bible. A seeker of truth cannot deny those truths.
The Bible has had more impact on western civilization than any other book. The Bible's emphasis on the belief in the one and only God has helped millions of people to turn away from worshipping idols and other false gods. Famous commandments like 'you shall not murder' have become universal principles. Many of the Bible's moral principles have helped to convert some of the worst people into compassionate, good citizens.
Obviously, if the Qur'an were to disagree with these moral and theological truths the Qur'an would have to teach the opposite of truth. This the Qur'an does not do. Where the Bible is true the Qur'an is also true, since they agree on many fundamental truths. This agreement, however, does not mean that one book copied out of another as some individuals are quick to conclude. This we have already demonstrated in our answer to Question 6. The reason the Qur'an agrees with the truths in the Bible is that those truths and the Qur'anic passages all come from the same source, namely God. Since He alone revealed the Qur'an and all the truths of the Bible, it is only logical that the truth will be one, regardless in which book it is found.
When the Qur'an disagrees with the Bible it is also for a reason. The Qur'an was revealed at a time when people knew the art of writing, and so designated scribes were able to write down the revelation immediately to ensure its preservation in written form. At the time people were also accustomed to memorizing eloquent compositions. With God's help they began a practice of memorizing the Qur'an, thus ensuring its preservation also in the hearts of millions of believers throughout history. Due to these two preservation methods, the Qur'an available all over the world today is the same in its original language whether you buy a copy in Canada, Australia, or China.
Therefore the Qur'an can be trusted in its entirety, and a believer can confidently say, "All of it is from our Lord" as the Qur'an states in 3:7. God has promised that He will safeguard the book (Qur'an 15:9). He further says that no falsehood can get into the Qur'an (Qur'an 41:42). He tells us that He sent the Qur'an to confirm the truth of what is in the previous scriptures and also to expose the errors that crept into those scriptures (Qur'an 5:48). So one reason the Qur'an differs from the Bible can be understood best in light of the transmission history of the two books.
Another type of difference between the two books pertains to the specific instructions that God gave. God always gives instructions which are suitable for the varying conditions of human life. Some of the instructions in the Bible, were meant for a particular historical circumstance, and are therefore no longer applicable. Since the Qur'an is newer, it contains God's latest instructions which are still applicable to our present conditions, and which provide the best solution for some of life's most pressing problems today.