The issue was to do with how I created my overlay. Pretty much I was using e.stopPropagation() to stop inner divs from closing on the overlay when the parent was clicked. Using e.stopPropagation() prevented some clicks of the wp editor from working.
Instead I used a check which would only apply the closing of the overlay on the parent, not the descendent elements which removed the use of e.stopPropagation().
$( "#parent_overlay" ).click( function( e ) {
//Without this check all inner elements would also apply the closing code
if( e.target == this ) {
$( "#parent_overlay" ).fadeOut();
$( "body" ).removeClass( "noscroll" );
}
});
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