Sorry, I do not understand the issue clearly. Can you please share some screenshots of the issue? And the code that creates the custom fields on your site.
Thanks, I understand the issue. The field type taxonomy does not work like a normal custom field, it does not save the value in the table wp_postmeta, it sets post terms. So if you want to use this field, please do not add it under a group as a subfield or save the field value to the custom table.
As I mentioned above, if you want to set post terms, please use the field type taxonomy. The field type taxonomy_advanced save the post meta like other custom fields, it does not set post terms.
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