it seems that the taxonomy field dont work inside the repeater field.
I like to create a metabox for concert tour dates.
So I create a custom taxonomy (VENUE).
Then I created a repeater-field inside I put the datepicker and the taxonomy-field (VENUE).
But the Venues are not stored in the repeater-field.
I’ve just tested in on my installation, but I couldn’t reproduce the issue. Could you please try to reproduce the issue on one of the WordPress’ stock themes (like Twenty Fifteen) with other plugins deactivated? If it disappears, then you can activate the theme and plugins one by one to see which one causes the issue.
It seems you have the “Load Terms” option enabled for your taxonomy. Because taxonomy field works individually, each of them will load the selected taxonomies. It won’t check if the other taxonomy fields are assigned to certain taxonomies. That’s why you have the first selected taxonomy on all of your taxonomy fields.
Kindly disable the “Load Terms” option to fix it. Keep in mind that you can’t update the taxonomy fields from the taxonomy meta box with this setup. But you still can update the taxonomy meta box with the taxonomy fields.