Same problem and this is what I've uncovered by reading various message boards. One of the message updates for iOS12 was a new feature that combines Message threads by iCloud account instead of the actual phone number. For me, I have our entire family (myself, wife, and kids) under my iCloud/Apple ID. This has caused massive issues and frustrations since the upgrade in that all of our texts are trying to combine in a single thread and we have no idea who is sending the text or who is supposed to receive the text.
From what I can uncover, Apple claims this was to help simplify viewing your texts over multiple devices (e.g. iPhone, iPad, etc.). However, there was already a previous feature in Settings to simply forward a text to other devices so I don't understand why Apple would force out this new combining feature.
My personal viewpoint is that Apple is trying to force every individual user to set up their own Apple ID and then connect them through the new Family Sharing feature. What they do not understand is that I am extremely uncomfortable with setting up my young children with an individual account connected to Apple.
If this is not reversed, then I will most likely leave Apple all together and finally jump over to Android. I will not be forced by Apple to allow them to connect directly to my minor children. That is highly arrogant of Apple to think they have the right to directly connect to a minor.