At a guess the cause is an uncompleted sync operation which leaves the records about what has and has not been transferred in an inconsistent state. Ideally iTunes would gracefully tidy up during the next sync, but it doesn't. 😕
Try the following all-purpose steps for dealing with erratic device or sync behaviour. They assume that all of the content you want on the device is in your library ready for restoring. If it isn't see Recover your iTunes library from your iPod or iOS device first. I would also recommend you copy everything out of the camera roll if you haven't already.
- Backup device.
- Restore as a new device.
- Restore the backup you made earlier.
Use an encrypted backup if you want to preserve passwords, Wi-Fi settings, web history and health data where appropriate. I also suggest syncing with a selection of playlists (unless you're using iCloud Music Library) rather than manually adding content as, if nothing else, the process above is easier to do if you ever have to go through it again.
tt2