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Why Wordfence Flags Thousands of Files After a WordPress Update (And How to Fix It)

41 threads Sep 16, 2025 Plugin → Wordfence security

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If you recently updated WordPress and were suddenly greeted by a Wordfence scan report listing thousands of "Unknown file in WordPress core" or "Old WordPress core file not removed during update" warnings, you're not alone. This is a common and often confusing scenario that many website administrators face. This guide will explain why it happens and walk you through the steps to resolve it.

What's Happening?

Wordfence Security works by comparing the files on your server against a known list of files that are supposed to be in a clean, official version of WordPress. When you update WordPress core, this list of known files also needs to be updated within Wordfence.

The most frequent cause of a massive spike in warnings is a temporary misalignment between the newly updated WordPress core files and Wordfence's internal known file list. This was a widespread issue reported by users after the WordPress 6.7 update, where scans falsely flagged over 2,000 legitimate core files as "unknown."

Common Causes and Their Solutions

1. Outdated Wordfence Rules (Most Common Cause)

Why it happens: The free version of Wordfence updates its firewall and scan rules every 30 days. If a major WordPress release happens within that period, Wordfence's list of what constitutes a "known" core file may not immediately recognize the new files.

How to fix it:

  1. Navigate to Wordfence > All Options > Advanced Firewall Options.
  2. Click the "MANUALLY REFRESH FIREWALL RULES" button.
  3. Run a new scan. This forces Wordfence to update its definitions and should clear the false positives.

2. Incomplete Core Update Process

Why it happens: Occasionally, the WordPress update process can be interrupted by server timeouts or file permission issues. This can leave old files behind that should have been deleted, triggering "Old WordPress core file not removed during update" warnings.

How to fix it:

  • You can often safely delete these leftover files. Wordfence may provide a "Delete all deletable files" button on the scan results page for these specific warnings.
  • For widespread issues (e.g., specific files like certain block editor CSS/JS files in WP 6.6), the WordPress core team might be aware of the bug and plan to remove them in a future update. You can safely ignore these specific files until the next update.

3. Host-Specific Modifications and Files

Why it happens: Some web hosts (e.g., GoDaddy Managed WordPress, IONOS) modify core WordPress files or add their own configuration files (like .orig backups or php.ini files) to core directories. Wordfence will flag these as modified or unknown.

How to fix it:

  • Do not delete host-added files like php.ini, as the host will likely just recreate them.
  • For modified core files, contact your host's support to ask why the modifications were made.
  • Within the Wordfence scan results, you can choose to ignore a specific file "until it changes" to prevent repeated warnings for known host modifications.

4. Cached Files from Performance Plugins

Why it happens: Performance plugins like WP Rocket or LiteSpeed Cache generate static HTML files and other data that are stored in your wp-content directory. Wordfence may scan these and report them if it's not configured to ignore cache directories.

How to fix it: You can exclude these cache files from future scans to prevent false alarms.

  1. Go to Wordfence > All Options > Scan Options > Advanced Scan Options.
  2. Find the "Exclude files from scan that match these wildcard patterns" field.
  3. Add the path to your cache directory on a new line (e.g., wp-content/cache/wp-rocket/* or wp-content/cache/litespeed/*).

When Should You Be Concerned?

While most of these mass warnings are false positives, it's crucial to remain vigilant. You should investigate further if your scan results include:

  • Files with clearly malicious code (like encoded strings designed to avoid detection).
  • Files in core directories with unusual names (e.g., lise8m.php in a CSS folder).
  • A small number of warnings instead of thousands, which is more indicative of a targeted compromise.

In these cases, the files should be treated as highly suspicious and removed immediately. If you are unsure, you can submit the file to a service like VirusTotal or seek assistance from a security professional.

Conclusion

Receiving a scan report with thousands of warnings can be alarming, but it is most often a temporary issue following a core WordPress update. The first and most effective step is almost always to manually refresh your Wordfence rules and run a new scan. Understanding the common causes behind these warnings empowers you to quickly resolve them and get back to maintaining your site's security with confidence.

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