Can only shut down Macbook Pro Retina 2013 forcefully

I have updated to the new OS X El Capitan 10.11 and my macbook pro retina early 2013 will not shut down properly. It is not every once in a while that it fails to shut down properly. It is every time, I have to force shut down the computer by holding the power button. When I try to shut down the macbook via "shut down" my desktop remains without any toolbar or icons. Please help!