HT204053 iTunes has synced my apps to a different phone with a different apple id

Question

I gave my old iPhone 4S to my wife a long time ago, and I set up an an iTunes account for her at the time.
When I connect her 4S to iTunes, iTunes tries to sync all my apps to her phone, despite us both having different Applle IDs.
We both have diferent iCloud accounts too, and we've used the same email address for this as the Apple ID.
Now I recently bought her the iPhone 5, and before I set this one up I backed up her old 4S via iTunes. Probably not the wisest move, given the history of syncing issues.
Anyway, everything seemed to be fine, until I noticed she had multiple updates to download for her apps. When she tried to update them, the iPhone 5 asked for her Apple ID, but displayed my Apple ID email address.
On further investigation, I discovered that her iCloud ID was actually my iCloud email address as well.
So, now I'm just confused, and I can't change either her iTunes ID or her iCloud ID on her phone. To make matters more confusing, when she's logged into iTunes, her Apple ID is correct, with the right email address for her.
Lastly, her iCloud email address, as listed on her phone, is a different email address of hers, and it can't be changed as it's greyed out.
I'm seriously frustrated by all of this, and I could really use some useful advice!
cheers

Answer 1

Starting with the fact that your apps have nothing to do with the cloud, we can proceed.
1. you can share your apple id for apps (that is itunes and apps store in settings) or you can use different.
If you are using different, she will not be able to update your apps, until she enters your password, cause they are yours and yours only. She can delete those apps from the phone and download new same once to her account, she will have to pay again if those are paid. To download fresh once to her account she will have to go to Settings> itunes and app store. and sign out of your apple id and sign in with hers.
2. She can not sign out of icloud on her phone, so you want to delete your icloud account from her phone only. Going to settings and icloud and press delete account. It will ask you if you want to keep the data or delete it and choice is yours. If you see your contacts on the phone, you delete, and then she can add new. If those contacts/calendars are hers, you keep.
Last note - logging in to itunes does not show or say anything about the phone, but as far as that if you guys really want to stay separate, you probably better off by creating new user account for her on your computer.