This is usually due to some of the details of Github’s authorizations for integrations. You can read about how we handle Github authentication and the permissions you grant us in our documentation.
In that article, we go over installing the Github app and granting access to either all repositories, or a specific repository. Pay close attention to the troubleshooting section, which probably has the information you need to figure out how to get those missing repositories showing in our setup wizard.
If this doesn’t help you get things working, you could try creating a site (using another repo or a manual deploy and let us know the API site ID in this thread, along with the intended repository to point to, and we can help set things up manually for you.