Suddenly, menu bar applications have blue badges
I see the same thing for Google Drive. Blue around the dots. I don't think this is a problem with your system, more that the highlight color selected in Preferences is being added to a menu item because of the way the company coded the app. Some apps are great at integrating (e.g. Dropbox, which went to great lengths to get a custom sidebar icon) and others are not (e.g. Google, which has weird bugs like this in the display of some apps).