EXTRA_FILE is a required file?

Lately, I've been getting an error saying that "There were problems with the code integrity check." on our Owncloud.
When I check the list of invalid files, it lists a .pem file in the cert folder. Problem is, the .pem file is what Owncloud is using as it's trusted certificate. I was wondering if there's any way to stop it appearing as an extra file?
My version is if that helps.
Thanks in advance for your replies.

can you try to perform a files:scan?

Thanks for your reply. I ran files:scan --all and nothing out of the ordinary appeared.

can you post the screenshot of the error message?,

there is also the option of adding this to your config.php