We are experiencing the same problem. Three phones updated to iOS 12 and they are all combining message threads. We've checked all contact info to make sure there is nothing in common and there isn't. We have three phones on the same Apple ID, but this isn't restricted to those numbers. My wife sent her friend a message from my phone to see if it would come through as me or her and it combined my wife's previous conversations into this new thread on my phone. I have tried manually entering my wife's phone number and it shows her name and then when I send the message it reverts to the thread with my daughter and my wife does not receive the message. This is a huge problem!!
Also, likely related, yesterday morning I started receiving messages on my Apple watch between my wife and her coworker- they never showed up on my phone, but I can see the full thread on my watch.
Apple has really dropped the ball on this update. It sounds like this was a bug on earlier releases and they didn't fix it prior to release.