From Clarification of the applicability of updates for the .NET Framework 4.6 and 4.6.1:
“Installing a security update for the .NET Framework 4.6 and 4.6.1 on a system that has an earlier version of the .NET Framework installed is unsupported and causes functionality problems.
[…]
Generally, customers on any given version of the .NET Framework should install only updates that apply to the target version of the .NET Framework that is installed on their system. Update installations that are intended for either a later version or an earlier version of the .NET Framework may not be blocked even though such an installation is unsupported. This unsupported state can be expected to cause functionality problems.“