Just to clarify, is this issue confined to any specific app? Do you receive any specific error?
Kindly ensure that you have granted the necessary permissions to the API scope.
Make sure that you are using the correct credentials when authenticating with the API. If you are using a certificate, make sure that it is valid and has not expired.
Regarding your domain being onmicrosoft, typically this should not affect the visibility of your API scope in "My APIs". Please doublecheck that you have configured your app registration to use the correct domain and tenant ID.
If you haven't done, you may refresh and re-try the steps.
If the issue persists, please share some more details of the issue and post a screenshot after concealing any private details.