Apps to lock screen asks for password after locking
This is a thing to do with the Secure/Smart Lock setup.  When using third party apps the system will default to the "primary" method (whatever you set as backup to finger print whether it is PIN, Password, or the draw on the screen gesture lock).  The only way I have seen to get around this is to grant root access to your Home Launcher (Nova does allow this in advanced settings), but it is not a guarantee with every device.  Here is what I found doing a quick Google search per your question: 
http://feedback.novalauncher.com/forums/145180-nova-feature-requests/suggestions/12241728-allow-lock-screen-function-to-be-unlocked-by-finge

Which does seem to indicate it is definitely more of an issue in Marshmallow (and probably future releases).  Hopefully enabling root MAY get you around this problem.