That's how it works. Touch something here, touch something there, learn from it and slowly build up the whole thing. I think Scrum and Kanban may work if you have a somewhat mature system where you add incremental features but if you do something relatively new and big the backlog can not reflect reality. Or it forces a workflow that doesn't make sense. I have seen it multiple times where people refused to make changes to something because their story was done already. Never mind that the design turned out to be unsuitable.