Unpublished products with Markets
In Shopify, you can choose whether to publish products to each market you create. This means that you don’t sell a product in all markets, you can unpublish those products from the markets that you don’t want it available to.
For more info, please visit https://help.shopify.com/en/manual/markets/publishing-products-with-markets.
There is a particular case when unpublished products are on the primary market. Usually, all products are published on the primary market, but you can decide that some products may not be temporarily available.
Frequently Bought Together provides support for this case via an Advanced Preference that you will have to check in case one or more products are excluded from the primary market.
In secondary markets, the app automatically checks the unpublished products, but in the case of the primary market, make sure you enable the check in the app preferences to ensure that the app does not display unpublished recommendations.
Note that it could take Shopify some time, usually two or three minutes, to update the state of a product after unpublishing it, and the app may display the unpublished recommendation.