City Info Tracker is undergoing a mild overhaul to correct many of the problems that cropped up at the time of Going Rogue's release. Previously, the system assumed that all Masterminds were Villains, and continues to make that assumption on the live version of the site.
For now, badges will need to be tracked with their Villain titles for Masterminds, but stay tuned because that should be changed sooner rather than later.