Assume that you send continuous instant messages (IMs) to a user in Microsoft Skype for Business 2016. Then you allow the toast notification window to be auto accepted. In the conversation window, you find every item but first gets duplicated. Also, in the Conversation History in Microsoft Outlook, you find that the conversation window shows duplicated IMs.
To fix this issue, install the January 3, 2017, update (KB3128049) for Skype for Business 2016.