Originally Posted By: Archeon
Originally Posted By: drakino
Did you ever plug in and back up your wife's device in iTunes on the same computer account? IE, do you and your wife share the same iTunes on the computer ... ?
Yes. Could that be a problem? (and her device is an iPhone, not an iPad)

Yes it can be. When you back up a device, it asks if you want to transfer purchases from the device back to the computer if the two aren't in sync. This includes apps with a prompt like this:

So an app backed up from your wife's phone is then saved on the computer in the shared iTunes library. Inside is a receipt tying the app to her Apple ID. When your device was restored, it pulled the apps from the computer and took her receipt with it.