Sorry to reply to this particular message but I couldn’t easily or quickly find a way to just generally add my feedback.
Here is the way it is happening on my family’s phones:
Phone 1 = iPhone 7, ios 12.0
Phone 2 = iPhone 7, ios 12.0
Phone 3 = iPhone 6s+, ios 11.2.6
All are on same Apple ID account.
Messages from phone 1 and phone 3 are combined in one thread to phone 2. Phone 2 does not combine with either of the other two. At least not yet. It combines whether iMessage is turned on or off (restarted with it turned off and it combined before it was turned back on). I believe it also impacts the Airdrop feature. I have tried most, if not all, of the possible or suggested fixes mentioned above (restart, delete threads, etc.). We have a group text between the three phones in which they all show up as a work-around for the moment. I understand if the problem is that Apple wants me to create more Apple IDs, but I do not want to do that. If, in the near future, there is not an option to turn this feature off, I will find a different way to communicate between the phones. Even if that means switching brands of phone. If the product is superior to the competition, there should be no need to try to prevent me from using a competitors product.
I think I included all the pertinent info. I just wanted to put it here so people can compare it to what else is going on and stuff like that. 😁