Hey,
I just ran into the same situation.
I added a check to see if the image was attached to a variant. Try to look for a section that looks like this in the product-template.liquid.
{% comment %}
Show other product images below product info if there's any left to show
{% endcomment %}
{% if index < product.images.size %}
{% for image in product.images offset:index_offset %}
**{% if image.attached_to_variant == false %}**
.....