Hi,
It must come from the bootstrap CSS of your template.
Any CSS from any part of your website can override the CSS of the HikaShop HTML elements.
So even if you set a specific size for thumbnails and that the thumbnail files are effectively the size you want, if you have something forcing the size of the thumbnails with CSS code, the browser will then adjust the size of the thumbnails on the fly.
Unfortunately, without looking at the page and analyzing the CSS of the element, I can't say much more than suppositions.