Home Screen and Recent Apps buttons don't work I am using Moto G3 TE. I was happy with the 5th version but because the frequent alert for 6th version was killing me, I gave up and updated to Marshmallow. It's been like 8 days and now my mobile is showing issues which I listed below:


Home Screen and Recent Apps buttons are not working. Though they show effect on touch but nothing happening.
I am unable to see Quick Settings through swiping from up to down
Pattern lock is not visible, when I press the lock button on side. My phone can be easily access by anyone now.
Moto's special feature of showing notifications on screen when I touch the phone, isn't working.


I am assuming the problem might be because of the upgrade to Marshmallow.

Other possible problems could be (considering today's activities):


Trying to upload around 2GB of data to Google drive. (When I tried this, unknowingly whole drives' data was downloaded to my phone until there was no space and then  the "DU battery saver" app crashed, this is the first issue I observed)
Giving some security permissions to "CM Security" app. 
Inserted micro USB pen drive and moved some files from internal storage to pendrive through inbuilt explorer.


What I tried (in sequence):


Uninstalled "DU battery saver" app.
Uninstalled "CM security" app.
Installed "Clean master" app.
Reinstalled "CM security" app.
I restarted my phone several times but no use.
I take off the screen glass from the screen, still no use. (unfortunately, the screen glass broken)
Tried to reset factory settings but it seems the "reset" button is disabled.
It seems I even can't able to do "Hard reset" which I tried by holding the lock and volume up button. The phone just gets restart. It is not that I want to do this but I just thought to give it a try.


PS: My phone is six months old.

Please help.
I was facing a similar error with the Nexus 5. Safe mode and wiping the cache partition were not working for me. People also complaining about not be able to use the adb commands because the phone does not connect.

One option I read about was doing a factory reset. This is probably not the preferred option so I found another one. This worked for me although it seems a little unconventional.


Download/install/open Nova Launcher
Long press on screen
Click on widgets
Create a nova activity
Scroll till you find setup wizard
Look for setup wizard test activity
Click on the icon you just created
Run through setup


I also read that it is caused by almost full storage. Unlike in the description I did not get a message telling that the storage is full and the phone is going into a mode optimized for low available storage. After, the phone rebooted (I also can't confirm that the phone rebooted).

Source: http://forums.androidcentral.com/android-6-0-marshmallow/600742-nexus-5-marshmallow-home-button-not-working-many-more-problems-3.html#post5344015

Nova Launcher: https://play.google.com/store/apps/details?id=com.teslacoilsw.launcher