There are number of reports regarding the frequent locations issue on iPhone on iOS10, the issue appeared to exists on all the iPhone models so this is a software bugs.
Most users have reported that on iOS10 the settings for Frequent Locations is off, doing a Reset for the location services will help to turn it on but the issue appeared to be continue after that too.
The issue is appeared to be on the upgraded models, the iPhone 7 doesn’t seems to have the issue since it comes with iOS10 installed.
One other fact is, if you try to fresh install the iOS10 on your old device the Frequent Locations appeared to be working fine.
Okay so here are the steps to fix this issue.
Let’s start with troubleshooting Location Services. Please reset your Location Services as described in the following article.
Reset or disable Location Services
Location warnings are the requests that apps (such as Camera, Compass, and Maps as well as location-based third-party apps) make to use Location Services with those apps. An app will ask for permission the first time it needs to access Location Services data.
Tapping Allow will give that app permission to use Location Services as needed. Tapping Don’t Allow will prevent an app from accessing Location Services data. Apps won’t use your location until they have asked for your permission and you grant permission.
If you would like to reset all of your location settings to the factory default, go to Settings > General > Reset and tap Reset Location & Privacy. When your location and privacy settings are reset, apps will stop using your location until you grant them permission.
After completing these steps, if the issue is still occurring you’ll want to look into saving a backup in iTunes and performing the steps in the Apple Support Article below.