Try this to add padding to the images:
.woocommerce div.product div.images .flex-control-thumbs li {
padding: 10px;
box-sizing: border-box;
}
Or go all out and try this for aligning the images to the left with padding:
.woocommerce div.product div.images.woocommerce-product-gallery {
display: flex;
}
.woocommerce div.product div.images .flex-control-thumbs {
order: -1;
flex: 1 0 25%;
display: flex;
flex-direction: column;
}
.woocommerce div.product div.images .flex-control-thumbs li {
width: 100% !important;
padding: 10px;
box-sizing: border-box;
}