Prerequisite warning check reported that "Proper version of IIS does not appear to be installed" during NFA 9.3 console installation. while IIS is already running on windows 2012 R2 server.
There may be parts of IIS which are not installed that are required. It is really easy to miss a Server Role or Feature on Windows 2012.
The documentation does a really good job of showing you where each and every prereq can be found.
Go through the two links below steps by step and verify all of the prereqs are installed then try again. The second link is the most detailed.
Install .NET Framework - CA Network Flow Analysis - 9.3.6 - CA Technologies Documentation
Install IIS, ASP, COM+, and SNMP - CA Network Flow Analysis - 9.3.6 - CA Technologies Documentation