Try using e.preventDefault();
:
$(document).on('keydown',function(e) {
//debugger;
if((e.keyCode == 68) && e.ctrlKey){
$('.duplicate').trigger('click');
e.preventDefault();
}
});
See demo page here (edit the demo here).
On a side note, it is not a good usability practice to override widely-known keys/commands. While you can achieve that, it is advisable and better to use another combination of keys.