I had problems triggering focus on an element (a form input) that was transitioning into the page. I found it was fixable by invoking the focus event from inside a setTimeout with no delay on it. As I understand it (from, eg. this answer), this delays the function until the current execution queue finishes, so in this case it delays the focus event until the transition has completed.
setTimeout(function(){
$('#goal-input').focus();
});