add_action('WCProductFilter_fields','WCProductFilter_field_my_custom_input', 30);
function WCProductFilter_field_my_custom_input(){

    $WCProductFilter = isset($_GET['WCProductFilter']) ? sanitize_text_field($_GET['WCProductFilter']) :""; // check this to ensure for is submitted from WCProductFilter.
    $_custom_input = isset($_GET['_custom_input']) ? sanitize_text_field($_GET['_custom_input']) :""; // Do not forget to sanitization

    if(!$WCProductFilter):
        $_custom_input = '';
    endif;


    /*
     *
     * you can check conditional here.
     *
     * if(is_shop()):
     * execute code only shop page
     * endif;
     *
     * */

    if(is_shop()):
        // this will only display under shop page and hide others page
        ?>
        <div class="field-wrapper">
            <div class="label-wrapper">
                <label class=""><?php echo __('Custom Input','wc-product-filter'); ?></label>
            </div>
            <div class="input-wrapper">
                <input type="search" placeholder="<?php echo __('Custom input','wc-product-filter'); ?>" name="_custom_input" value="<?php echo $_custom_input; ?>">
            </div>
        </div>
    <?php
    endif;

}


Use input field for query arguments


function wc_pf_query_args_custom_field($args, $form_data){

    //default search query
    $args['s'] = isset($form_data['_custom_input']) ? $form_data['_custom_input'] : '';

    return $args;

}
add_action('wc_pf_query_args', 'wc_pf_query_args_custom_field');