Yes. This is a direct answer because the distinction matters.
Automated scanners (Burp Suite Pro, OWASP ZAP, Nessus, Qualys) test for known CVEs in your technology stack. They check whether your framework version has a published vulnerability. They test for reflected XSS with standard payloads. They flag missing security headers. This is useful work and we run these tools as part of our engagement.
But a scanner will never discover that Tenant A can read Tenant B's invoices by changing an ID parameter from 10432 to 10433. It will never find that a viewer-role account can call the /api/admin/users endpoint because the authorization check only exists in the front-end React component. It will never test whether your Stripe webhook endpoint validates the signature before processing the event.
These are business logic vulnerabilities. They are unique to your application. No CVE number exists for them. No signature-based scanner can detect them. They require a human tester who reads your API documentation, understands your data model, creates accounts at different permission levels and methodically tests every boundary between what a user should access and what the application actually allows.
In our SaaS engagements over the past 12 months, 73% of critical findings were business logic flaws that no automated tool detected. The scanner found the missing HSTS header. The human tester found the tenant isolation bypass that would have exposed 40,000 customer records.
Run automated scans weekly. They are cheap and catch regressions. But do not mistake a green scan report for security. Get a human penetration test at least annually and after every major feature release. For API-specific testing, the gap between automated and manual testing is even wider.