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.
ruparocks
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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