Home Screen and Recent Apps buttons don't work
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