The Cross-Sell recommendation box will only show items you've manually defined them in the Upsell & Cross-sell. If you want to learn more about how to manually define cross-sell items with the upsell & cross-sell function, check out this article.

However, you may select a fallback option for your Cross-sell box.  The fallback option will allow the Cross-sell/Up-sell box to default to another automatically generated list of products when there is no Cross-sell/Upsell connection for a product. To learn more about Cross-sell/Up-sell fallback options, please click HERE.
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If the "Manual Picks - Include "Unpublished Collections" is checked for manually selected products for the Cross-sell and Upsell boxes in your Systems Configuration, the products will be shown in your Upsell and Cross-sell boxes. (This is checked by default. You can confirm this with our Support team)

For cross-sell bundles, the main item will not be included in the cart when the bundle is added even if the Manual Pick settings is checked.