When MalCare Flagged Clean Files as Malware and My Host Took the Site Offline — How I Proved the False Positive and Reinstated Hosting

It was a regular Wednesday morning when I received a chilling email from my hosting provider. They had taken my site offline “due to malware detected by an integrated security tool”—MalCare. As someone meticulous about maintenance and security hygiene, this came as a jolt. I hadn’t made any major changes recently, and everything had appeared normal. Little did I know this would spiral into a multi-day ordeal of proving that my site wasn’t compromised—and that an unfortunate false positive from MalCare was to blame.

TL;DR

MalCare mistakenly flagged core WordPress files and recognized plugins as malware in my installation. My host, relying on its automated tool, immediately suspended the site, which disrupted business for days. Through manual review and third-party scanning, I demonstrated the issue was a false positive. After some careful documentation and persuasion, my host reinstated the site and issued a warning to have manual oversight on similar issues going forward.

How Everything Unfolded

Imagine logging into your email and seeing the subject line: Your Website Has Been Taken Offline Due to Malware. My heart sank. Opening the email, my host explained they had automatically taken down the site after MalCare flagged suspected malware in several PHP files—including ones I knew were standard WordPress core or custom plugins I had developed myself.

Here’s what happened next:

• Within 5 minutes, I logged into the hosting dashboard. My entire public_html folder was quarantined. There was no access to site files unless I contacted support.
• In the control panel-log, MalCare had recorded over a dozen suspicious files, most of them inside wp-includes and wp-content/plugins.
• None were obviously malicious. Using FTP, I downloaded copies for review and ran them through various third-party scanners.

False Positive Red Flags

It quickly became evident that something was off. MalCare had flagged innocuous files—like wp-config-sample.php and files from well-known plugins including Yoast SEO. Even more baffling, a custom plugin I developed with no obfuscation and no external connections had been tagged “critical.”

I dug deeper and noticed that:

1. Some flagged files had base64-encoded content—but it was non-executable config information.
2. Others were simply larger PHP files, which apparently triggered MalCare’s heuristic pattern-matching algorithm.
3. Code snippets referenced common variables like $GLOBALS or eval, which by themselves, aren’t malicious.

After uploading these files to alternative scanners such as VirusTotal, Sucuri, and Quttera, all returned clean results. These tools scanned both the code and its behavior, and none flagged them as problematic.

Reaching Out to Support (And Getting Nowhere)

Hoping to resolve this fast, I contacted my hosting provider’s support. Their initial reply was apologetic but firm:

“We’re unable to reinstate your site unless MalCare shows no malware. We rely on their scoring engine for security flagging. You will need to restore from backup or replace the flagged files.”

This was infuriating—and a bit ironic. I had solid backups, but replacing files unnecessarily, especially when clean, didn’t sit well with me. Worse, they weren’t willing to question the automated tool.

How I Built My Case

With the host denying responsibility and MalCare providing no appeal channel, I took matters into my own hands:

1. Documenting Everything

I created a folder and saved:

• Screenshots of MalCare’s flagged list
• File hashes of the flagged files (MD5 and SHA256)
• Comparison reports between infected vs original plugin files
• Scan logs from VirusTotal, Sucuri, and other third-party scanners

2. Reaching Out to Plugin Developers

For the plugins that were flagged (Yoast SEO, Custom Post Types UI), I contacted the developers. They confirmed that the files hadn’t changed in months and were legitimate. They also expressed concern about MalCare potentially issuing false positives—which I learned, from online forums, was not unprecedented.

3. Creating a Comparative Audit

I setup a clean installation of WordPress on a subdomain and uploaded original plugin files. Then I ran MalCare again. Surprisingly, identical files were once again tagged!

This helped me prove that the issue wasn’t my installation—but possibly MalCare’s overly aggressive heuristic scan.

Getting the Hosting Provider to Listen

I drafted a concise report—less technical, more focused on the business impact. I included:

• Why the flagged files aren’t malicious
• Proof from trusted third-party scanners
• Confirmation from plugin developers
• A recommendation to manually review before auto-suspending live production sites

To my surprise, this got traction. Within 12 hours, I was escalated to Level 2 technical support, where an actual security engineer reviewed the case. After a day of back and forth, they acknowledged the files were misidentified by MalCare and reinstated the site.

Lessons Learned

This incident, though stressful, was a learning experience. Here’s what I took away:

Automation Isn’t Infallible

Security tools like MalCare significantly reduce manual effort, but they’re not immune to false positives. Blind reliance can disrupt businesses based on flawed detection logic.

Always Keep Backups and File Hashes

Because I had stored my own plugin files and knew exactly which versions were installed, I could assert their integrity. Backups let you restore, but file hashes help prove nothing was tampered with.

Host Communication Matters

Persistence paid off. Automated hosting support emails offer limited help, but escalating with a structured case and clear documentation gets results faster.

Consider Multi-Tool Validation

Relying solely on one scanner can be risky—using multiple tools gave me confidence and objective comparison to build my report.

Preventive Measures Going Forward

Post-recovery, I took extra steps to avoid a similar debacle:

• Installed logging tools like Wordfence and Query Monitor to detect real-time issues
• Setup alerts in my CI/CD pipeline to flag unexpected changes during deployment
• Built a simple shell script to generate daily file hashes and store them in the cloud
• Reached out to my host to exclude developer-specific directories from auto-scanning

Final Thoughts

This incident reminded me of one of the paradoxes in modern tech: while tools save us time, unverified automation can backfire spectacularly. MalCare remains a powerful solution, but as this experience shows, it’s not perfect. As site owners and developers, we need to hold tools accountable and make sure we have systems in place to distinguish a true infection from a false alarm.

If your site ever gets flagged wrongly, don’t panic—collect your evidence, use multiple tools, and make your case. Rationality and documentation can still break through a wall of automated decisions.