Shutting down my Mac Pro Retina properly?

When I shut down my Mac Pro, I close all apps except the Finder. I've noticed that sometimes when I start up again, the Apple logo and the loading bar don't appear, and when I go into the desktop, the Finder is still open on the folder it was on before I shut it down the last time. But there's still the normal start up sound. I think this is because when I see the screen go black, I close the laptop screen straight away, and it hasn't truly finished shutting down yet. I've been trying to wait for a minute before closing the lid after the screen goes black, and it's been working: the next time I start up my Mac the Apple logo and loading bar appears as usual, and when I get on to the desktop, the Finder isn't open on anything.
My question is, is it really bad for the Mac if I close the lid before it properly shuts down, and I leave it in a kind of limbo state before I start it up next time? Because sometimes I'm in a hurry and I don't have time to wait a minute before closing the lid.

Hello animefan4eva,
After reviewing your post, it sounds like you were trying to shut down the computer but closed the lid befor it finished. I would recommend that you read this article, it may be able to help the issue.
Mac notebooks: Wait for your computer to fully shut down before closing the display - Apple Support
If you close the display on a MacBook Pro, MacBook, MacBook Air, PowerBook, or iBook while it is shutting down, the computer may not shut down properly. 
Thanks for using Apple Support Communities.
Have a nice day,
Mario

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