Only one discount is applied after adding two bundles

Generally, the Shopify Discount system only allows one discount per order. There are only a few cases where two or more discounts can be combined, which are discussed in the Shopify documentation at https://help.shopify.com/en/manual/discounts/combining-discounts

Unfortunately, none of those options apply to two bundle discounts.

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