s96a non-material minor amendment applications - Public forum - Planning Advisory Service (PAS)

Can anybody advise whether there is a restriction on making a s96a application to a development that has already commenced and the amendment they are seeking already taken place? Logic would tend to suggest that as they have built something not in accordance with the approved plans that there is no planning permission for them to actually amend and therefore they need to apply for a brand new permission instead. I would be grateful for clarification.