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This happens a lot with the Shopify → Google app, even when everything *looks* published.
Google will simply skip any product that’s missing something it needs (GTIN/MPN, brand, size/color for apparel, or anything that triggers a policy review), but it won’t always show an obvious error in GMC.
Variants with messy data or no identifiers get ignored too. The easiest way to check is inside Shopify: go to Google & YouTube → Product Listings, click the missing product, and you’ll usually see why Google didn’t approve it.
Sometimes it’s as small as a missing barcode or the product not being set to the right target country.
