Use https://www.phpmyadmin.net/ or https://www.adminer.org/ (available on many web hosts or install yourself) and use the overall search function to search for an instance of the string domain.com/domain.com so you can the find the exact problem string, and also find which tables the ACF data is stored in. The strings might be in wp_posts, or wp_postmeta or even wp_options.
Once you find an instance of the bad string, you will see the exact format of the string – trailing slash, no trailing slash, etc – and you can try using Interconnect again, which is the safest method to correct the strings.
You can also manually edit each string in each database record with PHPMyAdmin or Adminer.
If Intercconnect doesn’t work for some reason, you can use a query such as
UPDATE wp_posts SET post_content = replace(post_content, 'http://domain.com/domain.com/', 'http://domain.com/');
in the SQL Query function in PHPMyAdmin or Adminer to bulk replace the strings. That query will find/replace post content in the wp_posts table. But simulate the query first in PHPMyAdmin or Adminer, and back up your database beforehand.
https://wp-cli.org/ is also a good choice, but you need to know that you are searching for the correct string before using WP CLI.