There has historically been a scaling issue when it comes to many of the relationship type fields. ACF is working within what is provided by WP. The taxonomy filter on the relationship field must get all of the taxonomies and then all of the terms in each taxonomy in order to sort them for the filter. This is also effected by the post types that can be filtered or the post type setting when filtering. This can be improved by limiting the post types and the taxonomies that appear in the filter. With a taxonomy with many terms in it has been reported that the request time out and showing no results. It may be necessary to limit the post types and not allow filtering by taxonomy on extremely large sites.
For more on this you should probably contact the developer here https://www.advancedcustomfields.com/contact/
