I’m having a similar issue and wanted to see if you could elaborate for me, Jonathan –
My site is using a WooCommere Products Of The Day extension on the product category pages (see here: https://dental.keystoneindustries.com/dental-supplies/) and for each product it’s giving it a nofollow link. As you mentioned, I did run a report on OnPage.org and was alarmed to see all the internal nofollow links, although they all point back to this extension on multiple pages.
Should I try and fix this or does it not really matter? Any advice would be appreciated.