Not really a bug. It is how all the note taking apps work.
Word processors like Word and Pages offer more control, but at the cost of being more “fiddly”. We are aiming to make editing very fast, so Agenda handles the numbering, and will terminate a list when it sees a paragraph of a different kind. This is usually what people want. You don’t want the list numbering running right through your long note, even in unrelated parts.
Appreciate the feedback, but for now we will keep it this way. Perhaps we can figure out some easy way to indicate the list should continue in future.