One weakness of a vulnerability scanner is that it is not designed to go through filters or bypass security controls like firewalls or intrusion detection systems. Vulnerability scanners typically perform well in identifying known weaknesses within the perimeter of a network or system but might not effectively assess systems that are shielded by robust security measures, which can filter out the scanner's attempts to probe or attack.
Reference:
National Institute of Standards and Technology (NIST), "Technical Guide to Information Security Testing and Assessment".