Product Upsell does checks to ensure that the user's cart qualifies for the offer before allowing customers to add a free product. However, it is not (and can never be) 100% foolproof due to the way Shopify accepts products and cart adjustments.
Upsell has an option, when you go to create the offer, that will remove the free items from the customer's cart when they no longer qualify under the offer's conditions. Visit Advanced Options in Product Upsell and What is the duplicate and hide feature? for more information on this functionality.
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