|The real "Msiexec.exe" is the executable for the windows installer. If it is deleted, you won't be able to add new software to your computer.|
However, there is this spoofed file (fake misexec.exe) that is carrying the same file name as the installer component on windows. This is the bad one, and is the one being detected as malicious exe by some antivirus. Some---because not all antivirus detects it as harmful, like AVG and symantec won't pick this up.
So how will you know if it's the real or genuine one? The real misexec.exe should only be running while you're installing something. It's also a Windows System File and should be in a system directory. In addition, it should have an installer-like icon. If it is, then this application is safe. You can know more about characteristics of malicious programs here.