Some files are missing after doing backup and factory reset on Android Lollipop
Google backup is unreliable and won't back up everything, however it should be fairly easy to make a backup yourself next time.

You can use ADB to make a full backup. You'll need to install ADB first: on Linux sudo apt-get install adb usually works, on Windows you'll need to download it from somewhere.

Turn on USB debugging (in developer options, to access go to settings > about phone and tap build number 7 times) and connect to a computer via USB. Then open a terminal/console window and do adb devices to check the phone's connected, and then adb backup -all -f C:\backup.ab (where backup.ab is the absolute path to where you want it backed up from).

Source: http://forum.xda-developers.com/galaxy-nexus/general/guide-phone-backup-unlock-root-t1420351