Apple ID appearing on another iPhone device (Sync confusion)

Issue

iTunes is sporadically requesting access to my partner's Apple ID account when downloading applications and trying to install the other iTunes account applications also when syncing takes place within iTunes. System software/accounts seems confused.

How can I ensure that both devices remain separate and do not access each other's iTunes accounts or sync over Mac logins? How can I delete mixed applications from separate Apple ID's ensuring it won't replicate the deletion on the primary Apple ID?

Background

• 1 x Macbook Pro OS 10.8.2
• iTunes 11.0.1
• App Store 1.2.1

• 1 x iPhone 4S OS 6.0.1 (Device A)
• 1 x iPhone 4 OS 6.0.1 (Device B)
• Separate Apple ID's
• Separate iCloud accounts

iTunes accounts

Both people have our own iTunes accounts linked to their own device. All details are currently correct when checking Apple ID profiles.

MacbookPro

Both people have separate MacBook Pro logins and software is all up to date.

History

In the past, over a year ago, both iPhone devices were sync'd via the same iTunes and Macbook log in. (Not a good start I know) Both iPhones always had their own iTunes account for downloading apps and music etc. When I realised I was syncing application data from one iPhone to the other on my Macbook, I created two Macbook log ins. I deleted all applications on Device B that were transferred from Device A and also deleted the applications in Device B's iTunes account. It seemed that both devices finally had seperated, retained their own Apple ID logins, applications and Macbook user logins.

Device B recently tried to install an application that Device A also had.

The application installed onto Device B without an issue and there was no confusion with Device A having the same application. The application can be upgraded to provide additional functionality. When Device B requested this within the application to upgrade, the Apple ID of Device A suddenly appeared.

I checked that Device B was asked to INSTALL the primary basic version of the application rather than OPEN it, just incase the confusion started at this point. It definitely said INSTALL.

I thought the divorce was done and dusted in the past.

Why would Device B suddenly point Device A's Apple ID?

To troubleshoot, I connected Device B to iTunes on the MacBook with Device B's Macbook log in. When iTunes opened within the Apple ID of Device B ALL DEVICE A applications appeared and started to sync these applications to Device B! I am back to mixed accounts.

How can ITunes suddenly connect the Apple ID's of both accounts and then tell Device B it needs to install Device A's applications? They are separate Apple ID accounts, separate copyright, separate costs.

I know with iMatch that you can share the library with another device and when this occurs it locks the Apple ID of the primary iTunes account for 90 days on secondary device. We have never done this.

I'm 'Syncing' trying to work this one out, please help!