All good books have various conflicts - both major and minor. It is interesting that you want information on a minor conflict. Let me give you two of them.
First, the main character, Jim Hawkins, is young. In the first few chapters he is a boy of twelve. He is easily frightened and at one point even runs to his mother. However, as the book progresses, he matures and becomes a young man. He bravely faces Silver and on a few occasions risks his own life. Therefore, one of the conflicts is internal. Will Jim be able to be a man with courage or remain a boy. In the end, he emerges as a mature young man.
Another conflict is when Silver and Jim come to the treasure site; they realize that it is not there. The reader is in a state of confusion. What makes matters worse is that the men with Silver are furious and they want to mutiny or even worse kill Silver and Jim. The question of where the treasure is is resolved as the reader finds out that Ben took the treasure and moved it.