The Exchange Team Blog has published a notice that .NET Framework 4.6.1 should not be installed on Exchange servers at this time:
In conjunction with .NET Framework 4.6.1, the databases may also be switched offline. The only remedy at present is to uninstall .NET Framework 4.6.1:
https://support.microsoft.com/en-us/kb/3095369
Currently, only .NET Framework 4.5.2 is supported for Exchange 2016 and Exchange 2013:
As Exchange updates are only released every 3 months, it will be a while before .NET Framework 4.6.1 is supported.
This article describes how the automatic installation can be prevented:
https://support.microsoft.com/en-us/kb/3133990
The registry key can also be imported directly via a .REG file:
Windows Registry Editor Version 5.00 [HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\NET Framework Setup\NDP\WU] "BlockNetFramework461"=dword:00000001
However, it is even easier using a group policy:
