I have the same issue. I updated to iOS 12, and everyone else on my iTunes/iCloud account in my family is being grouped into a single chat in Messages. So if I send "X" to my brother, "Y" to my father, and "Z" to my mother, all I will see is my mother's conversation at the top of my list in the main menu of Messages, and opening the conversation will reveal my last three texts being X, Y, and Z.
*An interesting fact to note is that my brother has not updated and is still running iOS 11.4. And yet, his messages are also being mixed with everyone else on the account.
- I have turned off iMessage completely and rebooted my iPhone. The issue persists.
- Send & Receive settings display just one phone number for each iPhone checked off.
- I do not have Family Sharing enabled (and I don't intend to do so in order to avoid this glitch).
- The Text Message Forwarding toggle is not present in my Settings app.
- Messages is turned off in iCloud settings on all devices.
- The person on iOS 11.4 has not had his conversations merged, but his messages are merged with other conversations on all iOS 12 devices.
- I will not accept any "fix" which involves creating new Apple ID's for everyone. I understand that it is strongly recommended, but I know a glitch when I see it, and I know there must be a way for separate phones with separate phone numbers to receive messages separately, despite being on a shared account.