This may be common, I did some searching but wasnt sure which terms to use. I'm no stranger to e-commerce, but I am new to Shopify. I've run a dozen successful shops on Bigcommerce, Woocommerce, and Volusion. As I create products I send them straight to search console for a manual crawl, it works great. With good SEO practices in the title and description, they usually hit on the first or second page within half an hour. I realized today as I was uploading urls that some of them were headed with product/ some were collection/ and some were the tag depending on the path followed to get to the product page. I already know that it will generate a different url based on how you get there for the same page, but I dont know how Google handles this. Does it care if half the URL's crawled are collections/ and the other half are products/ ? Will it all just work out in the end ? If I follow the trail through my collections if gives me the collection/ url. If I work through the menu link tree I had to create to simulate sub-categories, it gives me the product/ url. I would assume the product/ is ultimately the one I want.
Your theme is making use of the canonical url which sets the /products url as the default. This keeps Google happy and will avoid duplicate content issues. The /products url will also be what's used in the sitemap.