More specifically, it probably means you have automated discounts running at the same time.
In Shopify, you can't have both automated discounts + manual discount codes applied at the same time in checkout.
So what happens is:
(2) Trying to apply a discount which is no longer valid from items in your cart
The following scenario will make the error show:
* Add bundle discount eligible items to the cart
* Go to checkout
* See the discount code applied as expected
* Click back
* Change your cart to have no eligible items
* Click checkout > the result will be "X discount code isn’t valid for the items in your cart".
That's actually not app related.
The same thing will happen if you manually use a discount code which is no longer valid for the items in the cart.
Shopify saves the discount code inside the checkout page per session.
You can go ahead and test again with a new session through an incognito tab, that would help.