iMac not shutting down properly

Give this a try: boot into Safe Mode according to How to use safe mode on your Mac and test to see if the problem persists. Reboot normally and test again.

NOTE: Safe Mode boot can take up to 3 - 5 minutes as it's doing the following; 

• Verifies your startup disk and attempts to repair directory issues, if needed

• Loads only required kernel extensions (prevents 3rd party kernel/extensions from loading)

• Prevents Startup Items and Login Items from opening automatically

• Disables user-installed fonts 

• Deletes font caches, kernel cache, and other system cache files

Pay attention to the hard drives during the shutdown process.

If everything seems ok, when it happens next boot up.

• Select the pop up that states computer shutdown issue, it will present question to ignore or report.
• Select report to Apple, as this is not normal.

Make sure your system is up to date, and all apps too thru the App Store.