Forgive my vagueness about this because I don't remember exactly but I believe you have open one of the contacts and edit it. Once the edit screen is open, if there isn't a "linked contacts" option, tap the menu button. It may be in there. It took me a long time to find it myself. If I can find it again I will post the "how to" here for you. Good luck!
Found it! I'm on a custom rom so hopefully it is the same for you. Scroll through your contacts to the one you have mislinked. Top right corner of the screen is a chain link. Tap on that and the linked contacts come up. Tap on the link you want to break then tap done. They shouldn't be linked any longer.