The faith of many has been sabotaged as they came to something in scripture that went counter to their understanding or confused their theology.
There are several ways people approach this fairly common dilemma. Some study harder, read commentaries, search for explanations by others. This is often the right thing to do. We need to allow difficulties to motivate us to study. However, this can be a dangerous first step. Understanding scripture requires more than diligent study and natural intelligence. It calls for wisdom and spiritual insight. James says anyone who lacks wisdom should ask God. (James 1:5)
Sometimes people try to twist the scripture to say what they already think. I do not need to tell you this is wrong, but we certainly see it a lot.
I also see people getting louder in their affirmation of what a scripture seems to contradict. How many angry retorts have you heard against Paul’s statements about predestination (Eph.1:5) or some other doctrine that Scripture affirms or seems to put forth? Right or wrong this is unspiritual behavior.
Romans 12:14 tells us spiritual things are discerned by the Holy Spirit. He begins by bringing us to the point of meekness. We must submit to God’s truth no matter what. Then ask the Spirit to work patience in your heart to wait on His illumination. I recommend memorizing the verse or difficult passage. Then in patience and meekness meditate on it, praying for God to speak to your heart.
With this Spiritual foundation in place you can go to commentaries and study what others have written about a passage. It is interesting that commentaries seldom delve into passages that trouble us. But that will not keep God’s Spirit from giving you special insight into His truth.