This is one of the most troubling stories for me, and has always stood as a barrier between me believing in God. It has become an infamous story in the Hebrew Bible and one I'm not sure I'll ever understand.
"This is what the Lord Almighty says: ‘I will punish the Amalekites for what they did to Israel when they waylaid them as they came up from Egypt. Now go, attack the Amalekites and totally destroy all that belongs to them. Do not spare them; put to death men and women, children and infants, cattle and sheep, camels and donkeys.’" 1 Samuel 15: 2-3
God is commanding his chosen people to not simply kill the soldiers or those who are attacking, but to commit genocide on an entire race of people, killing even the innocent children and infants. When you take this and compare it to descriptions of God see in Psalms or his commandment to love your neighbor as yourself in Leviticus it becomes quite clear this is a contradiction. How does a loving, merciful God then order the genocide of a neighboring group of people? If your moral arbitrator is responsible for the deaths of children, is that someone you really want to follow? There may be a God but this is where the brazen truth and harsh reality sets in for me - if there is a God and this is what he is like that's still a God I don't want any part of.