Hi,
It comes from the customization done to the product page layout you have on your website.
The variants HTML data is inside the form of the product page:
i.imgur.com/VAuOXrD.png
Instead of being after it as it is the case by default:
i.imgur.com/tYwuIgP.png
demo.hikashop.com/index.php/en/hikashop/...with-characteristics
Because of that, when you click on the "add to cart" button, the product_id of all the variants is sent to the server:
i.imgur.com/98csaUE.png
And in that case, only the last one is taken into account by the server and thus HikaShop only sees the last one.
This indicates that some closing div tags are missing at the end of the view file that has been customized.
The best in such case is to contact the person who made the customization (someone on your end or your template provider) so that they can fix the HTML of the customized layout.
Since we don't know what exact change has been made, it's hard to say what should be done exactly.
I'm not even sure which layout you're using. I would guess "show_default" but it could be "show_tabular" too.