In Paulo Coelho's The Alchemist, there are two specific situations that can be identified as man vs society.
The first is when Santiago reaches the oasis. He sees an omen in the desert that he believes indicates the approach of war, even though the oasis is supposed to be a "neutral zone." Even with fear in his heart, Santiago approaches the leaders of the oasis to tell them what he has seen and that he believes danger approaches. Santiago is told that if he is wrong, he will be killed, but that they will act on his advice and prepare...and war does come to the oasis.
The second example is when Santiago goes with the alchemist out into the desert and they are taken prisoner by a group of soldiers. This is toward the end of the book. The alchemist tells the leader of their captors that Santiago (the boy) can turn himself into the wind. At this point, Santiago cannot believe that the alchemist would say such a thing: if the boy cannot turn himself into the wind, he will be killed by the soldiers, and Santiago fully expects to die at the hands of these men. Of course, Santiago ultimately does turn himself into the wind, thereby being saved.
In both of these examples, we see the conflict of man vs society.