Both Judaism and Christianity have wrestled with the conflict between the omnibenevolent, omnipotent and omniscient God who also allows evil and suffering. Throughout centuries philosophers, biblical scholars and theologians have tried to justify and respond to the contradiction by various arguments. The debate gave rise to the concept of Theodicy, an attempt to justify God's divine goodness with the existence of evil. For an overview of this topic see the Wikipedia article and the Cambridge Dictionary of Philosophy. There are also links to two streaming videos on this topic under the tab Videos & Media in this guide.
In addition, read an engaging essay by Joan Acocella, Misery: Is there a justice in the Book of Job? that sets the context for the contradiction of omnipotent God and the existence of evil as interpreted by thinkers and theologians throughout the centuries.