I have struggled a bit trying to understand while my Ubuntu 16.04 wasn't waking up with the common etherwake commad. I found the solution on this link:

you should disable Default option in Network-Manager GUI and enable only the Magic option. If you try this, then you should check if everything is ok opening the shell and issuing this command:

sudo ethtool <your_eth_device_here>

You should see the line:

Wake-on: g

If it's not g but d or something else, something could be wrong.

Once done that, and verified with the command ethtool <myNetinterface> | grep "Wake-on:", all started to work again :)