My app defines the intent filters to handle URL\'s from my site defined by
In our case we had 2 intent filters with applinks in our manifest: one with autoVerify="true" and one without.
So the verifier tried to verify domains for the 2nd intent filter and failed, and treated all our applinks as "not verified". You can find more details in this question.
You have to make sure every applink can be verified (which means adding assetlinks.json for every domain to be verified).