Why can't you delete an item, which content rights indicate you should be able to delete, only its subitems?
The user's effective rights to a content item are the runtime union of the rights to that item and the rights to that content item's current workflow state. If the user has read/write/delete rights on a content item, but that content item is associated with a workflow state to which the user doesn't have delete rights, even the final/done state, the user will not have the effective rights required to delete the item. The solution is to grant the appropriate rights to the workflow states as needed.