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

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.