By far the most important conflict of this time period was the Protestant Reformation. The Reformation completely remade Europe both politically and socially. Up until that time, the Catholic Church had been, for the most part, a unifying force in Europe. After the Reformation, religion became a dividing force. It helped cause conflicts between people and between states that came down on different sides of the religious dispute.
A related conflict was the Thirty Years’ War. This was, in part, a religious war. It pitted Catholics against militant Calvinists. However, the war was also about secular issues of dynasties and nationalism. By the end of this war, the Catholic monarchy in France was supporting the Swedes (who were Protestant) against the Habsburg Dynasty, which was Catholic.
From these examples, we can see that both religion and issues of politics and a desire for increased power were helping to cause chaos and disunity in Europe at this time.