You cannot only include sub fields when using an ACF form. ACF form can only work if the Repeater=>Group=>child fields are all shown and the structure is maintained. When you include only the child fields then ACF assumes that these will be saved at the top level rather than as rows of a repeater.
To to this you need to build your own form and then build an acf/save_post filter that takes the values submitted and updates the fields correctly.
