Customer is trying to buy two different subscriptions and Shopify Checkout is charging them shipping for each item separately. Why is that?

When customers are buying subscription products that are in the same delivery profile, coming from the same location, and you don't have any specific charge dates set in the subscription rule, then shipping for these products is consolidated together. If these conditions are not fulfilled, then Shopify will charge customer shipping for each subscription item separately. This is one of the limitations of Shopify Subscriptions and you can read about it here