I know this thread is old and long... But what worked for me, was unbinding FaceTime on the secondary phone. I signed out of just FaceTime. (I think someone has posted about this before)
Background:
I ran into this "shared' recent call history after upgrading to iOS9. Let me start by saying, I do not share my Apple ID with anyone but myself. I do, however have 2 phones, 2 Macs, 1 iPad. I didn't want the two phones to share the same recent call history, because that defeats the purpose of having two phones, from a phone perspective, while I do want both to be able to access iCloud services for other functions.
Steps of what I did (this is on iOS9, I don't recall if these are the exact same settings panes on iOS8, but the idea is the same. Also acknowledged that there are probably many steps that are unrelated, but I figured a methodic approach would remedy my issue.):
- On Phone 1, leave iCloud, App & iTunes Store, Message, FaceTime, all logged into iCloud.
- On Phone 2, log everything out of Apple ID:
- Signed out of Settings->iCloud, which will delete Mail, Contacts, Calendars, Reminders, iCloud Drive etc.
- Signed out of Settings->App and iTunes Stores
- Signed out of Settings->Messages->Send & Receive
- Signed out of Settings->FaceTime (I suspect this is the big culprit)
- Restarted both phones just to be thorough (probably unnecessary). Made a call from both phones to different places...the recent history isn't shared. One of the above things is causing the sync.
- On Phone 2:
- Signed into Settings->iCloud.
- Signed into Setting->App and iTunes Stores.
- Made calls from both phones, recent history still not crossed polluted! At this point, checked all my iCloud services work (Mail, Contacts, Calendar, iCloud Drive, etc) and I can access iTunes, Apps. iMessage also works, as long as I'm only using the Phone Number.
- Then I tested binding my Settings->Messages and Settings->FaceTime to my Apple ID. Call history started to sync again.
- Signed out of just Settings->FaceTime and recent call history stopped sharing.
FWIW, this will also disable some of the continuity features on the secondary device. I know for a fact, I used to have FaceTime enabled uniquely and the recent call history was not shared. So I'm still playing around to see if there is some sequence that can get this back.