Email account settings are included with the iTunes sync process if selected under Info tab for the iPhone sync preferences which transfers email account settings from your computer to your iPhone only. This is not a true sync process - email account settings are not transferred from the iPhone to your computer.
Apps will not be transferred from her iPhone by syncing her iPhone with your iTunes library - the apps on her iPhone downloaded with her iTunes account would have been deleted from her iPhone when syncing her iPhone with your iTunes library and iTunes account. The only way to transfer apps from an iPhone in that situation is by manually transferring all iTunes content from the iPhone with iTunes which would have required authorizing your computer with her iTunes account with iTunes first.
Contscts are synced with a supported address book app on your computer unless this is manually selected under the Info tab for the iPhone sync preferences with iTunes.
So what really happened?