A lot of "instinct" comes from experience. Having played and practices so much that you've seen everything. You know that the second hop behaves differently than the first hop, balls spin towards the line, a pop behind the plate comes back into play, or that low pitch will hit the dirt so take off for second... Basic info can be taught and learned, but to truly develop good instincts a player needs to be a student of the game at the deepest level.