Well I have read on many different websites that the philosopher's stone was not just an actual stone but the stone was the central symbol of the mystical terminology of alchemy, symbolizing perfection, enlightenment, and heavenly bliss. The stone can either be a real tangible stone or it could be part of the spiritual side of alchemy as a way to gain wisdom and enlightenment. I think that is what Nicolas Flamel meant when he "created" the stone.
Also if Nicolas Flamel did really create a stone it would have to be an incomplete stone because he knew that man kind was not able to with stand the power or wisdom that the stone held (and the fact that he died in his 80's). it's also said that an angel appeared before him and the angel "held a book in his hands and uttered these words, which were to remain in the memory of the hearer: "Look well at this book, Nicholas. At first you will understand nothing in it neither you nor any other man. But one day you will see in it that which no other man will be able to see." Flamel stretched out his hand to receive the present from the angel, and the whole scene disappeared in the golden light of dreams. Sometime after that the dream was partly realized.
One day, when Nicolas Flamel was alone in his shop, an unknown man in need of money appeared with a manuscript to sell. Flamel was no doubt tempted to receive him with disdainful arrogance, as do the booksellers of our day when some poor student offers to sell them part of his library. But the moment he saw the book he recognized it as the book that the angel had held out to him, and he paid two florins for it without bargaining." - from http://www.crystalinks.com/flamel.html
that's just my theory and opinion on the subject at hand.