One of the reasons we investigate the scriptures is so that we can make defense against people that may want to rubbish our faith, or to give adequate answers to those that do not understand our faith. Before we claim the Bible to be the final authority or free of error, we must know the basis for it i.e. we must thoroughly analyze and scrutinize the scriptures if we truly want to make the basis of our lives on the scriptures, for God's word cannot be separated from His systems, institutions, and reputation (John.17:17; Numbers 23:19).
In a sense, there are seemingly contradictions in the scriptures. However, we must be able to respond well by making an argument case for the scriptures to be true, because every seemingly contradiction can be explained if done thoroughly (1 Chronicles 22:25, 2 Samuel 24:29; John 20:1, Matthew 28:1, Mark.16:1). The seemingly contradictions is as a result of God's expression in His different dimensions e.g. God in the position of a Judge hates iniquities but in His merciful dimension, His love is expressed (Psalms 5:5; 1 John 4:8-11).
In establishing the idea of the infallibility of the scriptures, we must establish that the original manuscript, which 2 Timothy.3:16-17 spoke about, is true because it was inspired by God. However, in the passing down of the documentations about the scriptures, there may have been error because at different times were these books burnt down but it must be noted that the original manuscript is free of error. The Bible is infallible when it is put together.