Add custom email field input validation to check for unique email addresses for each field. You can add this to a site specific plugin.

ee_add_unique_attendee_validation.php

<?php
//* Please do NOT include the opening php tag, except of course if you're starting with a blank file

function ee_add_unique_attendee_validation(){
  wp_add_inline_script( 
    'single_page_checkout',
    'jQuery( document ).ready(function($) {
        $(".ee-reg-qstn-email").addClass("unique");
        $(".ee-reg-qstn-fname").addClass("unique");
        $(".ee-reg-qstn-lname").addClass("unique");

        $.validator.addMethod("unique", function(value, element) {
        var parentForm = $(element).closest("form");
        var timeRepeated = 0;
        if (value != "") {
            $(parentForm.find(":text")).each(function () {
                if ($(this).val() === value) {
                    timeRepeated++;
                }
            });
        }
        return timeRepeated === 1 || timeRepeated === 0;
        }, "* Duplicate! Please use a unique value");
    });'
  );
}
add_action( 'wp_enqueue_scripts', 'ee_add_unique_attendee_validation', 60 );