The ACF field values are requested from ACF via the get_field_object function, so we can not control what exactly is returned, that is for checkbox type or choice ACF field.
If you are using textarea, text input etc.. then only values from the database are selected. All the values that are present there are within the postmeta database for sure (because they are used), the plugin simply requests every possible value for that meta field. The extra values are within the database so they are displayed. Maybe a post was removed, but the values were not, or they are no longer assigned to anything else.
If you wish to add only a strict set of values, then probably adding them manually is the best idea.