Provide more details about those files being flagged. In some instances, if certain printer drivers are out of date (especially HP printer drivers) that message about files harming your computer come up pointing to those printer drivers. The cure here is to download the most current versions and reinstall.
Malwarebytes is a reliable product, but numerous users in the Apple Discussions have reported system corruption that has been traced to Clean My Mac, which some here have even referred to as malware.
By the way, when the MacOS intercepts something with that "will harm your computer" message it is preventing those files from being utilized in an installation. So it has prevented the malware, which is the built in MacOS security tool doing its job. What have you been installing recently on your Mac?
I would delete those specified files, empty trash, then reboot and see if things come up normally. Before doing that, I would completely uninstall Clean My Mac (this may take some detailed steps), then reboot, and if your MacOS without Clean My Mac still complains about those files, then delete them, empty trash, and see if it boots normally.
Unfortunately, sometimes people get into so much trouble with Clean My Mac that a reinstall of the MacOS is needed, hopefully that won't be the case with your system.