Fellow Exchange MVP Jaap Wesselius has written about reports of content index failures for Exchange servers that have been installed or updated with Exchange Server 2013 CU14 or Exchange Server 2016 CU3. Those cumulative updates were released by Microsoft in September of this year.
Although I have not personally observed the issue in the field, a number of customers are reporting the same issue in a Microsoft TechNet forums thread.
One customer who opened a support ticket with Microsoft has reported back to the forum thread to say that a bug has been acknowledged, and that the solution is to deploy a new Exchange server (either Exchange Server 2013 CU13 or Exchange Server 2016 CU2) and migrate mailboxes to the new server.
If you are experiencing the issue in your own production environment then I recommend you raise a support case with Microsoft to determine whether you are impacted by the same bug (don’t rely on blog posts or forum threads to confirm a production impacting issue).
If you are considering deploying a new server as the resolution to the issue then you can refer to my like for like Exchange migration article for some high level guidance.
Update: the indexing issues are reportedly fixed in the December 2016 releases for Exchange 2013 and 2016