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A pen test found what our scanner missed: what do we do now?

When a pen test finds a flaw your scanners missed, fix it, then work out why it was missed and what test would catch it next time. A short review method.

Safeguard Security Team
3 min read

Fix the issue first, then ask why your automated tools missed it. Most misses fall into a few groups: the tool never saw that code, it cannot detect that kind of flaw, or the finding was there and got ignored. Each group has a different fix, and none means the scanner is useless.

First, sort the miss

NIST SP 800-115 observes that scanners check for the possible existence of a vulnerability, while a penetration test's attack phase exploits it to confirm. Testers also look for combinations of weaknesses. So some misses are expected. Others are gaps you can close.

Why it was missedExampleFix
Out of coverageService or repo never scannedAdd it to the asset inventory and scans
Wrong test typeAccess control flaw between two usersAdd authenticated tests and manual review
Logic flawDiscount or approval flow abusedThreat model the flow, add a test case
Seen but ignoredFinding sat in a backlogFix the triage process or gate
ConfigurationScan could not log in, or skipped pathsRepair the scan setup and verify it
Too newDisclosed after the last scanIncrease scan frequency or add monitoring

A short review method

  1. Reproduce. Use the tester's steps to confirm the issue.
  2. Fix and retest. Get the tester or your team to verify. See pen test findings to fixed tickets.
  3. Check history. Search past scan results for the same issue or component. Was it reported and ignored?
  4. Name the category from the table above.
  5. Pick one preventive change: a new scan target, a regression test, a gate rule, or a threat model for that feature.
  6. Write a regression test where possible so the same bug cannot return unnoticed.
  7. Record it in the post-test notes with an owner and a date.

Do not overcorrect

Buying another scanner rarely fixes a logic flaw. NIST also notes that a second automated tool often reproduces the same false positives, and the same blind spots. Match the control to the cause. Read more scanners, more coverage: myth vs fact.

Try it yourself

Open the demo and look at how a code scan reports findings in a project. Ask which categories from the table a static scan could catch and which it could not.

Click through it at your own pace, or open it full screen.

Quick check

Does a miss mean our scanner is bad?

Not necessarily. Scanners and pen tests find different things. Treat each miss as information about coverage, test type or process.

Should we ask the tester to retest?

Yes, where the contract allows it. A retest turns a claim that it is fixed into evidence.

Safeguard focuses on the dependency and supply chain side, with SBOM scanning, reachability analysis and policy gates that keep known findings from being ignored. Try the free scan.

Sources

Last reviewed: 19 October 2026.

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