It simply means there is an app that is taking a while to shut down, or not responding to the remote shutdown command coming from the OS.
Mail.app is notorious for doing this, and happens fairly often to me on mine. And I shut down or restart regularly. 5-6 times a week. (I use DropBox Encore for an extra Dropbox account simultaneously, and Dropbox auto updates sometimes cause the Encore account to shut down, requiring a restart).
No big deal, but I've experienced the same phenomenon on all macs from the maxed out 27" iMac and 2016 15" MBP to my 2015 rMB. It can be irritating at times.