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).
It looks like you have the Appearance in the System Preference > General selected as Blue.
Try switching to Gray if you like it better.