Automated web application scanners have limitations in conducting comprehensive security assessments due to increasing complexities in web technologies. Scanners struggle with dynamic Ajax code, JavaScript obfuscation, complex session handling, backend APIs, and other emerging techniques. A better approach combines automated scanning with manual testing of known attack vectors, application profiling, input and output validation testing, and fuzzing to identify vulnerabilities beyond low-hanging fruit. Comprehensive security requires assessing how specific applications implement authentication, authorization, error handling, and defensive measures.