Hi,
Could it be that the "canonical URL" that you have entered in your products is wrong ?
In that case, the crawlers will try ot crawl these canonical URLs as you advertise them as being the main URLs of your product pages.
Besides that I don't see.
If the URL generates a 404, I suppose it's because sh404SEF didn't generate it and if sh404SEF didn't SEF (generate) it, it means that HikaShop didn't ask for that URL to be SEFed (generated). So that would mean that neither HikaShop not sh404SEF has any knowledge of these URLs and thus they would have been generated by something else on the website. Maybe a third party products display module ? Are you aware of something like that on your website ?