It looks like no one has responded to your question. Here are a couple things that might help others answer:
1. Is this duplication only happening with one sender, or is it happening with everyone that sends you an iMessage?
2. Is the conversation with duplicates a group message between several people, or just a conversation thread with one individual?
3. Did this just start recently, or has it been going on for a while? If it just started recently, did you make any recent changes, like updating your iPhone or changing your Apple ID?
4. If you go to Settings > Messages > Send & Receive, how many phone numbers/email addresses do you have listed under "You Can Be Reached By iMessage At"?