In Paulo Coelho's The Alchemist, there seem to be very few things that hold the character back from achieving his goals. In terms of personal "flaws," he trusts too easily and he experiences self-doubt after he is robbed.
When Santiago decides to sell his sheep, he is too quick to trust someone that he does not know. Part of the difficulty is that the bartender tries to warn Santiago, but they do not speak the same language. Santiago also does not spend much time in a community of people, traveling alone except for his sheep. This is not a personal flaw as I see it, but inexperience. He is disheartened and momentarily loses faith in himself—and this might well be seen as a personal flaw that temporarily stops his progress toward realizing his dream.
It might be considered a personal flaw that he believes that true wealth is found in things of material value. He does not understand that things of true value are often intrinsic in nature. However, one of Santiago's positive traits is his willingness to open his mind to new ideas, and he soon learns that he has been mistaken.
The other instance where Santiago is harshly tested, which stops his quest to fulfill his Personal Legend is when he goes to the crystal merchant for a job. Two important things happen here. First, the merchant tells Santiago that even if he worked for a year, he would still have to borrow money to travel to Egypt. At this moment everything the boy has learned and wished for almost ceases to exist.
There was a moment of silence so profound that it seemed the city was asleep. No sound from the bazaars, no arguments among the merchants, no men climbing to the towers to chant. No hope, no adventure, no old kings or Personal Legends, no treasure, and no Pyramids. It was as if the world had fallen silent because the boy's soul had. He sat there…wishing he had died, and that everything would end forever at that moment.
In this we see Santiago's complete loss of faith. The heroic young man with such towering aspirations and optimism is crushed in a single moment when an enormous obstacle appears in his path. This may well indicate a personal flaw: it certainly stops him from moving forward. In fact—and this is the second thing that happens—Santiago loses faith in his dream, his Personal Legend. In this instant he resolves to work for the crystal merchant to earn enough money to buy sheep and return to his old life.
This is exactly what Melchizedek, the King of Salem, had referred to when he had shared with Santiago the experience of the miner who had almost given up his Personal Legend after working so hard—and at this point Melchizedek had stepped in to help. However, this "flaw" in Santiago is understandable. His ability to overcome it takes eleven months. It seems, as is common in this story, that the universe "conspires" to help the boy achieve his goal. This time is well-spent in that he has the chance to think about his life, his goals, his strengths, and his dreams. He is also able to discover the universal language that leads him to watch for omens, as he tells the crystal merchant. Standing up to the merchant's suggestion that he return to his sheep, we see how much the boy has grown.
Whatever impediments that stand in Santiago's way because of his "flaws," he ultimately puts aside—he regains his faith in the world and himself, and is able to once again move toward his goal. Eventually the boy finds more wealth than he could have ever imagined.