I've run into this too and was also blaming it on Windows Phone 8, but I too am starting to think it's related to the People app in Windows 8 instead. I previously went through on my phone and manually checked each contact to fix the links... unlinking
contacts that were mis-linked, and linking ones that should have been.
Today I noticed contacts marked as Favorites that I know I did not mark, and lots of newly mis-linked contacts.
I noticed something of a pattern in that some contacts that were incorrectly linked were incorrectly linked in both directions. That is, the main display for "Person A" may have had 2 records that were actually "A" (let's say my Office 365 account and Facebook)
and an incorrect item from "Person B" (let's say Twitter). Looking at "Person B", they had 2 correct links (Office 365 & Facebook), and the Twitter account for "A". Hope that makes sense.
One other thing I'll throw in the mix... I have an Office 365 account (P1 plan) that is the same email address as my Microsoft account (aka "Windows Live", "Microsoft Passport", etc.). That has caused some sign-in weirdness over the year or so that I've
had it. Even though I have no contacts in my "Microsoft account" (what would be Hotmail or outlook.com), aside from the Facebook, Twitter, LinkedIn, etc. ones that have synced there, I wonder if there is something getting corrupt/confused going between my
account that exists in Office 365 and the Hotmail/outlook.com version.
It's all a mess and I can't even guess where I would begin if I tried to contact support. I think I'll try to hunt down all the various devices that may be syncing my contacts, remove the Windows 8 people/mail apps from all of them, check the DisplayName
attributes, do what I can to clean things up on my phone, then see about starting to reinstall the apps.