You should not normally see this message. Atlas applies all of your bundle offers through one shared Shopify automatic discount, Atlas Bundles Upsell Discount, so adding bundles or offers no longer uses up Shopify's automatic discounts one by one.
The message comes from a check left over from an earlier version of Bundle Deals, when each offer had its own discount. Atlas still counts the offers that were given their own discount back then. If those, together with the offers in the bundle you are publishing, reach 25, the publish is refused.
What to do
Start a chat from the bubble in the bottom right of Atlas, or email support@helloatlas.io. Include your store URL and the name of the bundle you are trying to publish, and a teammate will look into it.
ℹ️ Deleting other automatic discounts in your Shopify admin does not change this check. It only counts Atlas's own records from the earlier version.
See What is the Atlas Bundles Upsell Discount in my Shopify discounts? for how bundle discounts work today.