One possible reason why automatic discounts on Shopify POS cannot be applied is because they are available only for locations that have a Shopify POS Pro subscription. If you're not certain if you have the PRO subscription or not you can go to Shopify admin > Sales channels > Point of sale > Locations, there you'll see the type of the POS (see screenshot).
If you have the POS basic plan, you would need to upgrade to the POS Pro plan. This limitation is specific to the POS app and does not affect automatic discounts on your online store.
If you don't have the POS Pro plan subscription, then you will have to open the Bundler app tile in Shopify POS to apply the bundle discounts in Shopify POS.