I have the iPhone X, and I have noticed that it is not showing the App Clip via background NFC scanning. On the iPhone 11, my App Clip showed on tap. Devices older than iPhone X need to me scanned via the NFC reader in the Command Center, and it loads the App Clip.

Since my domain was valid, it took time for the Cache to resolve and update. To answer the question, you just need to give it some time.

Reading https://developer.apple.com/documentation/safariservices/supporting_associated_domains to see if I can understand the issue