Restore from backup not working?

Hi

So i went to the apple store yesterday to replace my iPhone 5 that had battery problems. I have applecare, so it was all good. BEfore they replaced it however, they made sure that i went home to back it up. So i did, and i made sure that i backed up everything, including the apps. So i went back to the apple store and got my new phone and it was all good. Then i came home and tried to restore it from backup, which it did for the most part. The only concern is that all my content on my 3rd party applications was completely erased. I am super upset about this, as i have very important files on it, and i thought that it would work. Is there anything i can do?

Thanks

Jacob