This is happening to me too. I’m glad I’m not the only one experiencing this. So far it has done this to me four times since installing iOS 12. Originally on my iPhone 7Plus and now my iPhone XS. The only contacts that it is doing this to me are my mother and father. They have separate apple IDs and separate phone numbers. I can have a thread with my mother and suddenly my father’s thread is gone and if I try to crest a new one it automatically reverts to the thread with my mother. His name or contact info is not on the thread at all. The only fix I have found is to delete the thread, delete both their contacts, then create new contacts for them and open new threads. That works for a couple days and then this again. It’s not that I have anything to hide from them, but it’s annoying and sometimes there’s things were discussing that the other wouldn’t know or care about.
Any ideas for a permanent fix or word from Apple on the matter?