I believe the warning you are seeing may be unrelated to your inability to Validate a SAML response. The Warning about duplicate certificates sounds like this issue:https://forum.mendix.com/link/questions/88536 so based on that perhaps the thing to try is to delete the SAML configuration from your admin page completely and start over with the IdP configuration.
Are you getting more details about why you are unable to validate the SAML response? There should be additional logging in the logs that give more detail about what went wrong when attempting to validate the SAML response. Depending on how far it got in the process, there may be actual messages in the SAML Admin page visible in your application front end. There is a Log tab on that configuration snippit that could give more information. I believe there may be two different things going on here.
Have you tried to adjust the logging level for the SSO module from Info to Trace? I've found much more useful info for troubleshooting after looking at the trace logs.