Other data can be lost App data. If you have removed an app and then restore from backup the App data may be restored, but since the App no longer exists, it won't show as being used anymore. The only way to remove that data would be to reinstall the app and then remove it.
An alternative to this would be to use the iCloud backup feature. If you are already backing up to iCloud, go in and unselect any apps you don't have installed. The alternative (or if you aren't already backing up to iCloud) is to turn off iCloud backup (wait a few minutes) and turn it back on. This will clear out old app data. You can also choose which data you want to get backed up as well. Then after the back is created, go to "Settings > General > Reset" and choose "Erase All Content and Settings". After the phone boots back up, choose to restore from iCloud.
Note, if that doesn't work and you need to set up the phone as new, you can save your Contacts in iCloud. Your pictures, you'll need to transfer to a PC. You'll need to manually reinstall your Apps from the App Store. Unfortunately, you'll lose all your stored messages.