If the required web application vulnerability scanner fails to run against your external endpoints, you should:
1. Use an alternative scanner such as OWASP ZAP, Burp Suite, HCL AppScan, or WebInspect.
2. File a support ticket to report the issue with the scanner so the relevant team (e.g., SR Ops) can investigate.
3. Perform the necessary scans using the alternative tool and include the reports in your submission.
If the required security scanner will not run against an external service's endpoint, you can use an alternative tool like OWASP ZAP, as long as you either own the external integration service or have permission from the service owner to perform the scan. Make sure to document the use of the alternative tool and any findings properly to align with the security review process.