Its not like they multiply is more that the thumbnails lose their class and style when the User change to a variation. I think it has something to do with line 84 in file /template/html/com_hikashop/product/show_block_img.php
Hmm, but on example page which you sent me... even when i change size I still see one main image and 2 images below. Or maybe you changed (fixed) something in meantime?