Malwarebytes Anti-Ransomware quarantined necessary files in WAMP server

I upgraded a localhost version of a Joomla 3.4.8 website to version 3.5. When I did Malwarebytes Anti-Ransomware quarantined some Apache files and a registration key.


When I tried to view the sites front end looked like this.


This all happened after the 3.5 upgrade and then I tried to update Akeeba. Mid way through I was warned by Malwarebytes Ransomware about the files. My other sites were still working fine.