Having same issue on my system. Win10pro x64. Current version of Malwarebytes Premium. The daily scan finds one potentially unwanted program that is a registry key, and 2 potentially unwanted modifications. I can exclude files, but when I check the boxes to the left of the threat scan results, the next button at the bottom right changes to "Quarantine Selected".
On the settings tab, under Exclusions. when I click Add Exclusion, there is no option listed to add a registry key or otherwise tell Malwarebytes Premium to not bring these 3 items up again. I have had this computer setup for over a year. No changes in this regard. All of a sudden a few weeks ago I get these threat scan issues.