This is probably because you have selected “Load Term” and “Save Terms”. This causes ACF to update the terms separately for each field and the only one that sticks is the last one. Basically, you can’t load and save terms when dealing with a repeater.
I’ve seen this discussed before, but I don’t know if it was ever solved by anyone.
I would probably turn off these settings for the taxonomy field and I would create my own acf/update_value for the repeater field that would set the post terms so that multiple terms can be added all at once https://codex.wordpress.org/Function_Reference/wp_set_post_terms
