Just has this happen to me. Thinking my NEW ASUS chromebook would automatically mute the speakers when I plugged in the headphones --- NO! I woke up my wife at 2AM, thanks ASUS!
The solution is to turn off the chromebook (close lid or switch off lower right) - plug-in the headphones, turn the computer back ON, it will search the I/Os and see the headphones are plugged in and mute the speakers.
It worked for me!