Thanks for reaching out to Microsoft Q&A.
Regarding the first issue, where an application is not listed in the CA Policy target, there's a limitation for Public / Native clients as this type of client won't be available for you when configuring the policy. The document below outlines that information so, if possible, make sure that the application is registered as a Web App in Entra
About the user behavior, we'd need to check exactly what's the CA that it's failing and its reason. Even though you were not able to configure your application there might be another setting on the CA affecting the user experience.
If you haven't done it already, check the properties as in the example below of the failing CA to check what exactly is making the CA to fail
Let me know if you have further questions.
Thanks,
Fabio