Assume that you create an instant message (IM) conversation with other users (either click Meet Now or invite more than three users to an IM conversation). If a user fails to accept the toast (for example, if the user is away from his or her desktop and misses the toast), a Missed Conversation item is written to Conversation History. But the first IM isn't recorded inside that Missed Conversation item.
To fix this issue, install the December 6, 2016, update (KB3127976) for Skype for Business 2015 (Lync 2013).
Note Lync 2013 was upgraded to Skype for Business in April 2015.