Only one discount is applied after adding two bundles

Only one discount can be applied to a single order. This is a known limitation of the Shopify Discounts system, as you can see at https://help.shopify.com/manual/promoting-marketing/discount-codes/discounts-faq#can-customers-use-multiple-discount-codes-on-a-single-order

For that reason, if a customer adds two discounted Frequently Bought Together bundles to a single order, only the second discount will be applied.