product-thumbnails.php

Original:
printf( '<a href="%s" title="%s" rel="prettyPhoto[product-gallery]" class="%s">%s</a>', esc_attr( $attachment_url ), esc_attr( get_the_title( $id ) ), implode( ' ', $classes ), wp_get_attachment_image( $id, apply_filters( 'single_product_small_thumbnail_size', 'shop_thumbnail' ) ) );

Replace with:
printf( '<a href="%s" title="%s" rel="prettyPhoto[product-gallery]" class="%s">%s</a>', esc_attr( $attachment_url ), esc_attr( get_the_title( $id ) ), implode( ' ', $classes ), wp_get_attachment_image( $id ) );